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nf-core_modules/tests/config/pytest_modules.yml

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Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
abacas:
- modules/abacas/**
- tests/modules/abacas/**
add module for abricate (#1280) * add module for abricate * rename abricate/abricate to abricate/run * Update test.yml Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-19 01:00:21 +00:00
abricate/run:
- modules/abricate/run/**
- tests/modules/abricate/run/**
abricate/summary:
- modules/abricate/summary/**
- tests/modules/abricate/summary/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
adapterremoval:
- modules/adapterremoval/**
- tests/modules/adapterremoval/**
Add AdapterRemovalFixPrefix (#1424) * Add AdapterRemovalFixPrefix * Prettifying Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
2022-03-21 10:26:12 +00:00
adapterremovalfixprefix:
- modules/adapterremovalfixprefix/**
- tests/modules/adapterremovalfixprefix/**
module for `agrvate` (#693) * initiate agrvate module * remove todos [ci skip] * remove todos and fix containers [ci skip] * ready for testing Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-16 10:42:23 +00:00
agrvate:
- modules/agrvate/**
- tests/modules/agrvate/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
allelecounter:
- modules/allelecounter/**
- tests/modules/allelecounter/**
Create ampir module
2022-05-25 11:27:10 +00:00
ampir:
- modules/ampir/**
- tests/modules/ampir/**
add module AMPlify (#1498) * add module AMPlify * Apply suggestions from code review Thanks for the review! Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * removed trailing whitespaces * Apply suggestions from code review Thanks again! Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * Apply suggestions from code review Thank you for the suggestions! Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Apply suggestions from code review Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * including review suggestions * fix versions.yml * add model_dir input * add model_dir to meta.yml * complete faa pattern in meta.yml * add fa.gz to pattern Co-authored-by: Moritz E. Beber <midnighter@posteo.net> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-20 09:53:26 +00:00
amplify/predict:
- modules/amplify/predict/**
- tests/modules/amplify/predict/**
add Amps (#768) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start work, continue once on non-mobile internet * finished and working on conda * Update modules/amps/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Apply suggestions from code review Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-09-30 10:54:16 +00:00
amps:
- modules/amps/**
- tests/modules/amps/**
add amrfinderplus module (#1284) * add amrfinderplus module * Update test.yml * Update main.nf * Update main.nf * Update test.yml * Update test.yml * Update test.yml * Update main.nf * Update meta.yml * Update meta.yml * Update main.nf * Update test.yml * Update test.yml
2022-02-19 23:02:23 +00:00
amrfinderplus/run:
- modules/amrfinderplus/run/**
- tests/modules/amrfinderplus/run/**
amrfinderplus/update:
- modules/amrfinderplus/update/**
- tests/modules/amrfinderplus/update/**
Initial module creation
2022-04-22 14:47:48 +00:00
antismash/antismashlite:
- modules/antismash/antismashlite/**
- tests/modules/antismash/antismashlite/**
add amrfinderplus module (#1284) * add amrfinderplus module * Update test.yml * Update main.nf * Update main.nf * Update test.yml * Update test.yml * Update test.yml * Update main.nf * Update meta.yml * Update meta.yml * Update main.nf * Update test.yml * Update test.yml
2022-02-19 23:02:23 +00:00
Antismashlite download databases (#1426) * Create module antismashlitedownloaddatabases * Corrected user-specification of database directory * Updated test.yml * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Fix typo in test.yml * Feed database files via docker/singularity mount) * Add external db file mounts to the containers * Fixed docker command in main.nf * Apply prettier * Apply prettier and add PWD * Add more output to test.yml * Add more output paths to test.yml * Fixed test.yml * Apply suggestions from code review Add documentation of why we need to mount files to the containers. Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Fix code linting errors (remove trailing whitespaces) * Fix code linting error (remove trailing whitespace) * Fix errors from Prettier linting Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-21 08:38:17 +00:00
antismash/antismashlitedownloaddatabases:
- modules/antismash/antismashlitedownloaddatabases/**
- tests/modules/antismash/antismashlitedownloaddatabases/**
add module for ariba (#1731)
2022-06-15 16:18:31 +00:00
ariba/getref:
- modules/ariba/getref/**
- tests/modules/ariba/getref/**
ariba/run:
- modules/ariba/run/**
- tests/modules/ariba/run/**
Added module arriba (#611) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-22 14:19:42 +00:00
arriba:
- modules/arriba/**
- tests/modules/arriba/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
artic/guppyplex:
- modules/artic/guppyplex/**
- tests/modules/artic/guppyplex/**
artic/minion:
- modules/artic/minion/**
- tests/modules/artic/minion/**
ASCAT (#1332) * First commit * putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it * adding first try of relevant commands (not working yet, just took their basic pipeline example * test commit * remove test * starting up work with module after 3.0.0 upgrade * add ascat.prepareHTS statemet * add location of docker for new mulled alleleCounter+ASCAT container * first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam * add notes on dropbox download * use a newer pytest_modules.yml * add outpit * trying to align with current Sarek output * adding in FH comments * busy clearing up arguments and testing. Still WIP * first working run, in nextflow, with sarek-like output. Still needs more work on input arguments * cleaning up before writing up findings * testing with putting in arguments in args * draft for solution 3 style for arguments * one more test added * adding FH map * finished testing maps for args * wrap-up cram/crai test successfully * updates to address ability to put in ref.fasta argument for cram running * adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config * first test with auto-downloading the s3-data (when not given as an argument) * removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug * adding mulled singularity container * removing tests * fix left padding lint issue * lint failure in meta.yml * more linting errors * add when argument * adding stub functionality * add stub run * correct md5sum for versions.yml * more testing with -runstub * stub code in pure bash - not mixed with R * reformat version.yml * get rid of absolute paths in test.yml * correct wrong md5sum * adding allelecount conda link * rename normal_bam to input_bam etc * let the pipeline dev worry about matching the right loci and allele files * dont hardcode default genomebuild * adding download instruction comment * add doi * fix conda addition bug * add args documentation * test new indent * new test with meta.yml indentation * retry with new meta.yml * retry with new meta.yml - now with empty lines around * retry with new meta.yml - remove trailing whitepsace * trying to fix found quote character that cannot start any token error * try with one empty line above triple-quote and no empty line below * trying with pipe character * checking if its the ending triple quote * one more try with meta.yml * test update bioconda versioning for linting failure * test update bioconda versioning for linting failure 2 * testing allelecounter version error on conda Co-authored-by: @lassefolkersen Co-authored-by: @FriederikeHanssen
2022-03-15 10:18:43 +00:00
ascat:
- modules/ascat/**
- tests/modules/ascat/**
add new assembly scan module (#971) * add new assembly scan module * add newline endings * fix newline ending * add newline at end Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-29 08:01:23 +00:00
assemblyscan:
- modules/assemblyscan/**
- tests/modules/assemblyscan/**
Add new module 'ataqv/ataqv' (#998) * Add new module 'ataqv/ataqv' * Update main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 12:51:40 +00:00
ataqv/ataqv:
- modules/ataqv/ataqv/**
- tests/modules/ataqv/ataqv/**
Ataqv mkarv (#1857) * first draft * fix test run * Apply suggestions from code review Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update tests/modules/ataqv/mkarv/test.yml * Update tests/modules/ataqv/mkarv/test.yml * Update tests/modules/ataqv/mkarv/test.yml * Update tests/modules/ataqv/mkarv/test.yml * Update tests/modules/ataqv/mkarv/test.yml * Update modules/ataqv/mkarv/nextflow.config * Delete nextflow.config * Update tests/modules/ataqv/mkarv/test.yml * fix linting * fix linting Co-authored-by: bjlang <> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-07-07 20:40:31 +00:00
ataqv/mkarv:
- modules/ataqv/mkarv/**
- tests/modules/ataqv/mkarv/**
Add atlas/call (#1809) * Add atlas/call * Apply suggestions from code review * Update modules/atlas/call/main.nf Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com> * Apply suggestions from code review Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>
2022-07-01 13:06:07 +00:00
atlas/call:
- modules/atlas/call/**
- tests/modules/atlas/call/**
Add Atlas/PMD (#1810) * add atlas/pmd * update atlas/pmd tests * Add atlas/PMD module * Remove comment * Run Prettier * Incorporate Review by @jfy133 Co-authored-by: maxibor <maxime.borry@gmail.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-24 14:53:51 +00:00
atlas/pmd:
- modules/atlas/pmd/**
- tests/modules/atlas/pmd/**
Create atlas/splitmerge Module (#1756) * Add atlas/splitmerge module * Finish the tests for atlas/splitmerge * Prettier * Update modules/atlas/splitmerge/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Remove curly brackets from meta.yml parameters For single-file outputs, as reviewed * Lintung: Remove trailing white-space Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-13 13:09:32 +00:00
atlas/splitmerge:
- modules/atlas/splitmerge/**
- tests/modules/atlas/splitmerge/**
add bakta module (#1085) * add bakta module * Update main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 12:17:25 +00:00
bakta:
- modules/bakta/**
- tests/modules/bakta/**
Add module: bamaligncleaner (#676) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add bamAlignCleaner module * Add container tags * Update modules/bamaligncleaner/main.nf
2021-09-15 08:31:49 +00:00
bamaligncleaner:
- modules/bamaligncleaner/**
- tests/modules/bamaligncleaner/**
bamcmp (#1244) * New module added bamcmp Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
2022-02-02 16:38:41 +00:00
bamcmp:
- modules/bamcmp/**
- tests/modules/bamcmp/**
New module: `bamtools/convert` (#1219) * 📦 NEW: Add bamtools/convert module * 👌 IMPROVE: Update output channel name, Add tests for each output format * 👌 IMPROVE: Add error test * 🐛 FIX: Remove custom tags Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-28 09:58:25 +00:00
bamtools/convert:
- modules/bamtools/convert/**
- tests/modules/bamtools/convert/**
New module: `bamtools/split` (#798) * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update with new versions.yml file * 🐛 FIX: Update meta.yml + correct typos * Update modules/bamtools/split/meta.yml Add bam, split, chunk tags Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 🐛 FIX: Correct meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-12 12:43:08 +00:00
bamtools/split:
- modules/bamtools/split/**
- tests/modules/bamtools/split/**
Add `bamutil/trimbam` (#1060) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add bamUtil trimBam * Update modules/bamutil/trimbam/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/bamutil/trimbam/main.nf * Changes after code-review * YAML lint Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-11-15 16:44:12 +00:00
bamutil/trimbam:
- modules/bamutil/trimbam/**
- tests/modules/bamutil/trimbam/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bandage/image:
- modules/bandage/image/**
- tests/modules/bandage/image/**
Module to map reads with BBMap (#717)
2021-09-20 09:27:34 +00:00
bbmap/align:
- modules/bbmap/align/**
- tests/modules/bbmap/align/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bbmap/bbduk:
- modules/bbmap/bbduk/**
- tests/modules/bbmap/bbduk/**
Add bbmap/bbsplit module (#771) * Add bbmap/bbsplit module * Conda complains about md5sum * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-30 12:37:35 +00:00
bbmap/bbsplit:
- modules/bbmap/bbsplit/**
- tests/modules/bbmap/bbsplit/**
Bbmap index (#683) BBMap index module
2021-09-03 07:28:28 +00:00
bbmap/index:
- modules/bbmap/index/**
- tests/modules/bbmap/index/**
feat(bbmap): Initialize pileup module (#1441) * feat(bbmap): Initialize pileup module * test(bbmap): Update outputs * test(bbmap): Add pileup tags * style(bbmap): Add in when Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-03-24 23:38:24 +00:00
bbmap/pileup:
- modules/bbmap/pileup/**
- tests/modules/bbmap/pileup/**
bcftools/annotate ready2go (#1291) * bcf annotate ready2go * edited output name * fixed output * updated bcftools ver * changed contain output string * removed contain key entirely * fixed md5sum for test.yml Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-28 13:23:12 +00:00
bcftools/annotate:
- modules/bcftools/annotate/**
- tests/modules/bcftools/annotate/**
Add bcftools/concat module. (#641) * draft for bcftools modules [ci skip] * initial test for bcftools concat * Update the params for testing * fix tests * Accomodate code review [ci skip] Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update the meta file and open PR for review * Update the keyword * Update the tags for module [ci skip[ * add threads Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-08-10 13:10:27 +00:00
bcftools/concat:
- modules/bcftools/concat/**
- tests/modules/bcftools/concat/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bcftools/consensus:
- modules/bcftools/consensus/**
- tests/modules/bcftools/consensus/**
bcftools/filter:
- modules/bcftools/filter/**
- tests/modules/bcftools/filter/**
Add bcftools/index (#812) * feat: add bcftools index * Extend tests to also test gen for TBI * Update meta.yml * Update meta.yml
2021-10-13 08:40:04 +00:00
bcftools/index:
- modules/bcftools/index/**
- tests/modules/bcftools/index**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bcftools/isec:
- modules/bcftools/isec/**
- tests/modules/bcftools/isec/**
bcftools/merge:
- modules/bcftools/merge/**
- tests/modules/bcftools/merge/**
bcftools/mpileup:
- modules/bcftools/mpileup/**
- tests/modules/bcftools/mpileup/**
Add bcftools/norm module (#655) * Initial draft [ci skip] * trigger first test * update output file path * Tests passing * finishing touches for meta.yml and update checksum * tweak checksum * add threads to the module * skip version info for matching test md5sum [ci skip] * Add ref fasta and finalize the module Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-16 15:40:03 +00:00
bcftools/norm:
- modules/bcftools/norm/**
- tests/modules/bcftools/norm/**
Add bcftools/query module (#670) * initial commit [ci skip] * add basic structure [ci skip] * finalized the bcftools/query module * add optional files [ci skip] * Add the vcf index file as param [ci skip] * update the md5sum for output file [ci skip] * all tests passing
2021-09-14 07:19:01 +00:00
bcftools/query:
- modules/bcftools/query/**
- tests/modules/bcftools/query/**
Add bcftools reheader (#585) (#608) * local tests and linting passing (#585) * fix: picard filtersamreads input (#610) * Move readlist into same input channel as bam * Update test reflecting input restructuring * Update tests/modules/picard/filtersamreads/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix test Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added module arriba (#611) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * added test for new header * enhance module fastp: add `save_merged` (#598) (#614) * enhance module fastp: add `save_merged` (#598) * removed md5sum checks from log and json * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
2021-07-23 21:24:19 +00:00
bcftools/reheader:
- modules/bcftools/reheader/**
- tests/modules/bcftools/reheader/**
add tests
2022-05-20 14:46:19 +00:00
bcftools/roh:
- modules/bcftools/roh/**
- tests/modules/bcftools/roh/**
create modules
2022-05-20 11:34:54 +00:00
Bcftools sort new syntax (#1169) * Added files for bcftools/sort * Fixed output format and removed md5 checksum * Change input to avoid identical in/output names * Created rows for bcftools/sort in pytest_modules.yml
2022-01-05 11:15:54 +00:00
bcftools/sort:
- modules/bcftools/sort/**
- tests/modules/bcftools/sort/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bcftools/stats:
- modules/bcftools/stats/**
- tests/modules/bcftools/stats/**
Add bcftools/view module (#669) * initial commit [ci skip] * add stubs [ci skip] * Finalize the bcftools/view module * accomodate optional files * add optional region file * refer the targets file in the tests * all tests passing * documen the optional parameters
2021-09-12 17:51:40 +00:00
bcftools/view:
- modules/bcftools/view/**
- tests/modules/bcftools/view/**
Module/bcl2fastq (#1883) * add bcl2fastq * test fixes * fixed tests * add tests to workflow * change container source
2022-07-14 11:18:21 +00:00
bcl2fastq:
- modules/bcl2fastq/**
- tests/modules/bcl2fastq/**
Module/bclconvert (#1485) * bclconvert: initial commit * add most of tool * attempt at adding testing stub * add dockerfile + instructions * add container to module * update readme * more attempts at making stubs work * finish stub run * fix ci issues * more fixes to stub * add read version check to stub * fix some tests * update readme * fix version number * syntax fix * revert edit to output directory * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/bclconvert/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update meta.yaml * update thread usage * Update modules/bclconvert/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> * Escape env variable * Update modules/bclconvert/Dockerfile Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com> * fix comments by @Emiller88 * fix task.cpus Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 13:39:22 +00:00
bclconvert:
- modules/bclconvert/**
- tests/modules/bclconvert/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bedtools/bamtobed:
- modules/bedtools/bamtobed/**
- tests/modules/bedtools/bamtobed/**
bedtools/complement:
- modules/bedtools/complement/**
- tests/modules/bedtools/complement/**
bedtools/genomecov:
- modules/bedtools/genomecov/**
- tests/modules/bedtools/genomecov/**
bedtools/getfasta:
- modules/bedtools/getfasta/**
- tests/modules/bedtools/getfasta/**
bedtools/intersect:
- modules/bedtools/intersect/**
- tests/modules/bedtools/intersect/**
Add bedtools/makewindows module (#658) * Add bedtools/makewindows module
2021-09-07 18:36:06 +00:00
bedtools/makewindows:
- modules/bedtools/makewindows/**
- tests/modules/bedtools/makewindows/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bedtools/maskfasta:
- modules/bedtools/maskfasta/**
- tests/modules/bedtools/maskfasta/**
bedtools/merge:
- modules/bedtools/merge/**
- tests/modules/bedtools/merge/**
bedtools/slop:
- modules/bedtools/slop/**
- tests/modules/bedtools/slop/**
bedtools/sort:
- modules/bedtools/sort/**
- tests/modules/bedtools/sort/**
added bedtools split
2022-05-17 12:24:32 +00:00
bedtools/split:
- modules/bedtools/split/**
- tests/modules/bedtools/split/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bedtools/subtract:
- modules/bedtools/subtract/**
- tests/modules/bedtools/subtract/**
Add centrifuge module (#1410) * Add centrifuge module * Add centrifuge module * Add centrifuge module * Add centrifuge module
2022-03-18 14:39:27 +00:00
biobambam/bammarkduplicates2:
- modules/biobambam/bammarkduplicates2/**
- tests/modules/biobambam/bammarkduplicates2/**
add module: biobambam/bammerge
2022-05-16 12:39:58 +00:00
biobambam/bammerge:
- modules/biobambam/bammerge/**
- tests/modules/biobambam/bammerge/**
New tool: biobambam/bamsormadup (#1478) * add bamsormadup * fix yaml * add test.yml * Update tests/modules/biobambam/bamsormadup/test.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * test meta.yaml: remove md5sums * Tool bamsormadup: - add (optional) reference input - add bam index ouput - add cram output option - make metrics output: more general * fix input and output formats * update input file description * drop sam output, goes against nf-core regs; add input check for cram files * fix typo * Update modules/biobambam/bamsormadup/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * improve ref fasta name * fix if else shorthand * fix syntax error * kind of fix tests * set fixed suffix for metrics file to keep it in line with picard and bammarkduplicates2 * fix command line * update test.yml * add support for multiple input bams * Update modules/biobambam/bamsormadup/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/biobambam/bamsormadup/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/biobambam/bamsormadup/test.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-06 06:18:23 +00:00
biobambam/bamsormadup:
- modules/biobambam/bamsormadup/**
- tests/modules/biobambam/bamsormadup/**
Add core Biscuit tools (#1354) * create files with nf-core command * update meta.yml files * starting to work on index main.nf * prelim test for index * index test working; not finding all output files * index passing tests * index and align passing tests * prototyping biscuitblaster and pileup * update containers * updates to pileup * pileup passing tests * template creation for more biscuit tools * tests passing on blaster,bsconv,pupsom * epiread passing tests, but need to update SNP bed file path * vcf2bed working; change test file * all biscuit commands passing tests * biscuitblaster rename * try to fix permissions * more permission fixes * trying a couple more permission changes * hopefully last permission fixes * really last permission changes * few more permissions * add when blocks * Remove read group meta Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * remove read group meta Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * changes for first round of review * update meta.yml with more specific links * Update modules/biscuit/biscuitblaster/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Apply new version reporting Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/biscuit/pileup/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update main.nf * Update modules/biscuit/pileupsomatic/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * update test file path * Update modules/biscuit/align/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/biscuit/align/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * tests passing again * Update modules/biscuit/align/main.nf * Update modules/biscuit/bsconv/main.nf * Update modules/biscuit/epiread/main.nf * Update modules/biscuit/index/main.nf * Update test.yml * Update modules/biscuit/pileupsomatic/main.nf * remove module-specific extension/prefix * remove module-specific extension/prefix * add missing args * switch pileup strategy * update test.yml * remove debug * whitespace cleanup * add in newline escapes * requested changes * Update modules/biscuit/pileup/meta.yml Co-authored-by: Spix <nathan.spix@submit.cm.cluster> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Spix <nathan.spix@node107.cm.cluster> Co-authored-by: njspix <nathan.spix@vai.org>
2022-03-14 13:34:22 +00:00
biscuit/align:
- modules/biscuit/index/**
- modules/biscuit/align/**
- tests/modules/biscuit/align/**
biscuit/biscuitblaster:
- modules/biscuit/index/**
- modules/biscuit/biscuitblaster/**
- tests/modules/biscuit/biscuitblaster/**
biscuit/bsconv:
- modules/biscuit/index/**
- modules/biscuit/bsconv/**
- tests/modules/biscuit/bsconv/**
biscuit/epiread:
- modules/biscuit/index/**
- modules/biscuit/epiread/**
- tests/modules/biscuit/epiread/**
biscuit/index:
- modules/biscuit/index/**
- tests/modules/biscuit/index/**
biscuit/mergecg:
- modules/biscuit/index/**
- modules/biscuit/mergecg/**
- tests/modules/biscuit/mergecg/**
biscuit/pileup:
- modules/biscuit/index/**
- modules/biscuit/pileup/**
- tests/modules/biscuit/pileup/**
biscuit/qc:
- modules/biscuit/index/**
- modules/biscuit/qc/**
- tests/modules/biscuit/qc/**
biscuit/vcf2bed:
- modules/biscuit/vcf2bed/**
- tests/modules/biscuit/vcf2bed/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bismark/align:
- modules/bismark/align/**
- modules/bismark/genomepreparation/**
- tests/modules/bismark/align/**
bismark/deduplicate:
- modules/bismark/deduplicate/**
- tests/modules/bismark/deduplicate/**
bismark/genomepreparation:
- modules/bismark/genomepreparation/**
- tests/modules/bismark/genomepreparation/**
bismark/methylationextractor:
- modules/bismark/methylationextractor/**
- modules/bismark/genomepreparation/**
- tests/modules/bismark/methylationextractor/**
bismark/report:
- modules/bismark/genomepreparation/**
- modules/bismark/align/**
- modules/bismark/deduplicate/**
- modules/bismark/methylationextractor/**
- modules/bismark/report/**
- tests/modules/bismark/report/**
bismark/summary:
- modules/bismark/genomepreparation/**
- modules/bismark/align/**
- modules/bismark/deduplicate/**
- modules/bismark/methylationextractor/**
- modules/bismark/summary/**
- tests/modules/bismark/summary/**
blast/blastn:
- modules/blast/blastn/**
- tests/modules/blast/blastn/**
blast/makeblastdb:
- modules/blast/makeblastdb/**
- tests/modules/blast/makeblastdb/**
bowtie/align:
- modules/bowtie/align/**
- modules/bowtie/build/**
- tests/modules/bowtie/align/**
bowtie/build:
- modules/bowtie/build/**
- tests/modules/bowtie/build_test/**
bowtie2/align:
- modules/bowtie2/align/**
- modules/bowtie2/build/**
- tests/modules/bowtie2/align/**
bowtie2/build:
- modules/bowtie2/build/**
- tests/modules/bowtie2/build_test/**
Add bracken (#1423) * feat: add template for Bracken * chore: update version * refactor: change command build * refactor: rename report variable, change quotes * docs: remove refactored input parameter * fix: correctly assign arguments to options * tests: set up single and paired end tests * style: apply prettier * chore: change data sources to official ones * refactor: rename test workflows * tests: use correct input to the new UNTAR module * chore: update md5sums
2022-03-22 15:40:21 +00:00
bracken/bracken:
- modules/bracken/bracken/**
- tests/modules/bracken/bracken/**
Busco module commit with nf-core v2.2 c1
2022-01-27 14:36:18 +00:00
busco:
- modules/busco/**
- tests/modules/busco/**
module: bwa/aln (#624) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add bwa/aln module * Also output reads as required with SAI * fix container paths * Sync bwa version samese/sampe * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-27 07:13:48 +00:00
bwa/aln:
- modules/bwa/aln/**
- tests/modules/bwa/aln/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bwa/index:
- modules/bwa/index/**
- tests/modules/bwa/index/**
bwa/mem:
- modules/bwa/mem/**
- tests/modules/bwa/mem/**
module: bwa/sampe (#625) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add bwa/aln module * Also output reads as required with SAI * Add sampe * Fix container paths * Update based on code review from @grst * Update input docs
2021-08-02 13:37:48 +00:00
bwa/sampe:
- modules/bwa/sampe/**
- tests/modules/bwa/sampe/**
module: bwa/samse (#626) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add bwa/aln module * Also output reads as required with SAI * Add bwa samse * Fix container paths * remove TODO comment * Updated based on code from from @grst on bwa/sampe * Clarify output docs
2021-08-02 13:21:23 +00:00
bwa/samse:
- modules/bwa/samse/**
- tests/modules/bwa/samse/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
bwamem2/index:
- modules/bwamem2/index/**
- tests/modules/bwamem2/index/**
bwamem2/mem:
- modules/bwamem2/mem/**
- tests/modules/bwamem2/mem/**
bwameth/align:
- modules/bwameth/align/**
- tests/modules/bwameth/align/**
bwameth/index:
- modules/bwameth/index/**
- tests/modules/bwameth/index/**
CAT CAT (#722) * bbmap/align done * Tests for single end and prebuilt index * Write bam file directly * Forgot to use all cpus for bbmap * Test md5sums * Added pigz support * Update modules/bbmap/align/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * process_medium and fastq * cat/cat module * Remove filter from CAT_CAT Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-20 20:02:22 +00:00
cat/cat:
- modules/cat/cat/**
- tests/modules/cat/cat/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
cat/fastq:
- modules/cat/fastq/**
- tests/modules/cat/fastq/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
cellranger/count:
- modules/cellranger/count/**
- tests/modules/cellranger/count/**
- modules/cellranger/mkref/**
- tests/modules/cellranger/mkref/**
Add Cell Ranger mkfastq, mkgtf, and count (#979) * feat(cellranger): Add initial count module Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * feat(cellranger): Add mkgtf module * test(cellranger): Fix count test with mkgtf * fix(cellranger): Generalize gtf attribute filters * chore: Add .gitignore for cellranger tar * build(cellranger): Update dockerfile https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/ * Apply suggestions from code review Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/cellranger/mkgtf/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * style: Capitalize README * test(cellranger): Update pytest_modules * feat(cellranger): Add initial mkfastq module * ci: Update pytest modules * refactor(cellranger): Update modules to new syntax * docs(cellranger): Update meta files There is some terrible copy-pasting going on. * fix(cellranger): Add args Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
cellranger/gtf:
Add Cell Ranger mkfastq, mkgtf, and count (#979) * feat(cellranger): Add initial count module Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * feat(cellranger): Add mkgtf module * test(cellranger): Fix count test with mkgtf * fix(cellranger): Generalize gtf attribute filters * chore: Add .gitignore for cellranger tar * build(cellranger): Update dockerfile https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/ * Apply suggestions from code review Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/cellranger/mkgtf/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * style: Capitalize README * test(cellranger): Update pytest_modules * feat(cellranger): Add initial mkfastq module * ci: Update pytest modules * refactor(cellranger): Update modules to new syntax * docs(cellranger): Update meta files There is some terrible copy-pasting going on. * fix(cellranger): Add args Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
Fix modules warned or failed with nf-core modules lint (#1191)
2022-01-03 18:00:46 +00:00
cellranger/mkfastq:
- modules/cellranger/mkfastq/**
- tests/modules/cellranger/mkfastq/**
cellranger/mkgtf:
- modules/cellranger/mkgtf/**
- tests/modules/cellranger/mkgtf/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
cellranger/mkref:
new module `cellranger mkref` (#896) * add cellranger mkref module * add cellranger mkref tests * update test yml chksum * fix module linting * fix test yml * fix getprocessname * fix versions typo * fix cellranger test.yml * fix versions.yml * test versions.yml * fix grep version * fix cellranger version * add dockerfile and readme * review container statement * Update modules/cellranger/mkref/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * add disclaimers * change location dockerfile Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-28 11:33:57 +00:00
- modules/cellranger/mkref/**
- tests/modules/cellranger/mkref/**
Add Cell Ranger mkfastq, mkgtf, and count (#979) * feat(cellranger): Add initial count module Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * feat(cellranger): Add mkgtf module * test(cellranger): Fix count test with mkgtf * fix(cellranger): Generalize gtf attribute filters * chore: Add .gitignore for cellranger tar * build(cellranger): Update dockerfile https://joshtronic.com/2021/09/12/fixed-repository-debian-security-buster-updates-changed-suite-from-stable-to-oldstable/ * Apply suggestions from code review Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/cellranger/mkgtf/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * style: Capitalize README * test(cellranger): Update pytest_modules * feat(cellranger): Add initial mkfastq module * ci: Update pytest modules * refactor(cellranger): Update modules to new syntax * docs(cellranger): Update meta files There is some terrible copy-pasting going on. * fix(cellranger): Add args Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-12-02 14:27:20 +00:00
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
new module `cellranger mkref` (#896) * add cellranger mkref module * add cellranger mkref tests * update test yml chksum * fix module linting * fix test yml * fix getprocessname * fix versions typo * fix cellranger test.yml * fix versions.yml * test versions.yml * fix grep version * fix cellranger version * add dockerfile and readme * review container statement * Update modules/cellranger/mkref/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * add disclaimers * change location dockerfile Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-28 11:33:57 +00:00
Update centrifuge/centrifuge (#1495)
2022-04-07 09:46:34 +00:00
centrifuge/centrifuge:
- modules/centrifuge/centrifuge/**
- tests/modules/centrifuge/centrifuge/**
Add centrifuge module (#1410) * Add centrifuge module * Add centrifuge module * Add centrifuge module * Add centrifuge module
2022-03-18 14:39:27 +00:00
New module: `checkm/lineagewf` (#899) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Added but test failing due to null on output channel * fix prefix variable * Complete checkm_lineagewf * Remove TODOs * Add description of fasta_ext parameter * Improve meta map for this context * Update meta.yml * Update modules/checkm/lineagewf/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2021-10-26 20:54:10 +00:00
checkm/lineagewf:
- modules/checkm/lineagewf/**
- tests/modules/checkm/lineagewf/**
Chromap Module (#659) * Initialise chromap module * Revert "Initialise chromap module" This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b. * Remake chromap base files with new layout * Copy chromap * Copy index * Add compression * Update padding * Update container * Update chromap input test data * Add chromap chromap tests * Add padding * Update comment * update yaml file * Remove TODOs * Add fasta input to yaml * Update YAML * Remove comment, update container * Remove comments * Import Chromap index * Update test.yml * Fix read input * Update test.yml * Add bcftools/concat module. (#641) * draft for bcftools modules [ci skip] * initial test for bcftools concat * Update the params for testing * fix tests * Accomodate code review [ci skip] Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update the meta file and open PR for review * Update the keyword * Update the tags for module [ci skip[ * add threads Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add module for dragonflye (#633) * add module for dragonflye * fix tests for dragonflye * Update test.yml * Update meta.yml * Update main.nf * Update main.nf * Update modules/dragonflye/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * update typos. change quote from ' to ". (#652) * Add bcftools/norm module (#655) * Initial draft [ci skip] * trigger first test * update output file path * Tests passing * finishing touches for meta.yml and update checksum * tweak checksum * add threads to the module * skip version info for matching test md5sum [ci skip] * Add ref fasta and finalize the module Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Expansionhunter (#666) Please enter the commit message for your changes. Lines starting * adds expansionhunter module Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update test.yml (#668) * Specify in guidelines one should split CPUs when module has n > 1 tool (#660) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Describe CPU splitting * Update README.md Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * More CPU examples Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Add dsh-bio export-segments module (#631) Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * update: `BWA/ALN` (#653) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Remove reads from output channel following module guidelines. Should do a .join() based on $meta, to reassociate. Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * Update seqwish reported version to match bioconda version. (#678) * Bbmap index (#683) BBMap index module * Initialise chromap module * Revert "Initialise chromap module" This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b. * Remove unnecessary files * Remove unnecessary files * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/chromap/chromap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/chromap/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove pytest_software.yml * Apply suggestions from code review Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: JIANHONG OU <jianhong@users.noreply.github.com> Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 16:20:55 +00:00
chromap/chromap:
- modules/chromap/chromap/**
- tests/modules/chromap/chromap/**
chromap/index:
- modules/chromap/index/**
- tests/modules/chromap/index/**
add clonalframeml module (#974) * add clonalframeml module * Update main.nf * try recommended gzip * Update main.nf Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-15 19:43:53 +00:00
clonalframeml:
- modules/clonalframeml/**
- tests/modules/clonalframeml/**
Add new module: cmseq/polymut (#918) * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs/outpus * remove trailing whitespace * first cmseq commit * compressing and removing not reproducible md5sums * save intermediate work * follow symlinks while decompressing * add cmseq/polymut * add polymut * add extra test with optional input file * remove metabat2 * Update modules/cmseq/polymut/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix file extension * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add test without bam index * split tests in workflows * answer PR review * report version from variable Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-09 15:12:51 +00:00
cmseq/polymut:
- modules/cmseq/polymut/**
- tests/modules/cmseq/polymut/**
added new module cnvkit/antitarget
2022-05-23 14:52:06 +00:00
cnvkit/antitarget:
- modules/cnvkit/antitarget/**
- tests/modules/cnvkit/antitarget/**
CNVkit: Make targets file optional when running in WGS mode (#1030) * Make targets.bed optional when running in wgs mode * added test for cram * Update test_data_config with new reference.cnn * Update main.nf to allow tumor-only running Still need a unit-test for this. Almost ready, but needs this file as input https://github.com/nf-core/test-datasets/blob/modules/data/generic/cnn/reference.cnn * re-writing previous changes, but now it wont crash the entire CI-setup * fixing overlooked merge conflict * last overlooked merge-conflict * move all files to batch subfolder * adding an optional input for a reference file (needed when running germline and tumoronly) * minor typo * update meta.yml * aligning code, renaming cnvkit to cnvkit_batch, renaming tumorbam to tumor, normalbam to normal * Update pytest_modules.yml Co-authored-by: EC2 Default User <ec2-user@ip-172-31-21-198.us-west-2.compute.internal> Co-authored-by: Lasse Folkersen <lassefolkersen@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 19:56:57 +00:00
cnvkit/batch:
- modules/cnvkit/batch/**
- tests/modules/cnvkit/batch/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
add new module cnvkit/reference
2022-05-23 16:35:50 +00:00
cnvkit/reference:
- modules/cnvkit/reference/**
- tests/modules/cnvkit/reference/**
controlfreec significance (#1451) * controlfreec significance * move freec files to own subfolder * Fix meta.yml naming * Fix meta.yml naming * Fix linting * Forgot to refactor * forgot more refactoring * Too much refactoring on output paths * Too little refactoring here * update checksum
2022-03-25 17:22:17 +00:00
controlfreec/assesssignificance:
- modules/controlfreec/assesssignificance/**
- tests/modules/controlfreec/assesssignificance/**
controlfreec/freec:
- modules/controlfreec/freec/**
- tests/modules/controlfreec/freec/**
add controlfreec (#1333) * add drafty controlfreec * get sofatware version * use maps in map * update paths to new and soon-to-be merged test files, add more input docu * Stab at documenting args map * Update syntax * Bit more description * Make the linter happy * tests pass locally * Add outputs & docu * tests are failing locally now :/ but cpn file can also be added * All tests passing, need to update test data again to add folder * Clean up files * Clean up files * Clean up files * Don't know how to get the test to run with the direcotry for now. they pass locally though * Make linter happy * Name process back * Update to use tar folder * fix the checksum
2022-02-28 18:08:58 +00:00
add freec2bed script (#1453)
2022-03-25 19:31:52 +00:00
controlfreec/freec2bed:
- modules/controlfreec/freec2bed/**
- tests/modules/controlfreec/freec2bed/**
add freec2circos script (#1454) * add freec2circos script * remove todo statements
2022-03-26 20:25:29 +00:00
controlfreec/freec2circos:
- modules/controlfreec/freec2circos/**
- tests/modules/controlfreec/freec2circos/**
add makegraph script (#1452) * add makegraph script * allow renaming of output files * allow renaming of output files
2022-03-25 19:49:08 +00:00
controlfreec/makegraph:
- modules/controlfreec/makegraph/**
- tests/modules/controlfreec/makegraph/**
Cooler cload (#634) * rebuild cooler cload. * update test file path of cload. * add pytest for cload * update to version.yml * update the test data path * Update tests/modules/cooler/cload/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Update modules/cooler/cload/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Update tests/config/test_data.config Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * Update main.nf Remove a lonely curly bracket. * Update test.yml Updated with new workflows. * update the test files * merge the conflicts. * update the test.yml * update for change of cooler/dump Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 21:43:55 +00:00
cooler/cload:
- modules/cooler/cload/**
- tests/modules/cooler/cload/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
add gatk4/gatherbqsr (#1130) * nf-core modules create * add module files * indent * remove templte code * manually revert pytest changes from tools * manually revert pytest changes from tools * add include statement back in Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-12-08 22:43:36 +00:00
cooler/digest:
- modules/cooler/digest/**
- tests/modules/cooler/digest/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
cooler/dump:
- modules/cooler/dump/**
- tests/modules/cooler/dump/**
Cooler merge (#515) * add software/cooler * fix the wrong files uploaded. * create a branch for cooler/merge * remove the bin_size from metadata. * update the test_data to test-datasets * update pytest_modules.yml * update the test file from single input file to two input file. update the output file from hdf5 to bedpe. * update the version.txt to version.yml and functions.nf * change version.yml to versions * update the test file path and fix the output versions. * Update meta.yml Correct "version" to "versions" * Update main.nf Fix typo * Update main.nf Remove some spaces Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-15 15:18:43 +00:00
cooler/merge:
- modules/cooler/merge/**
- tests/modules/cooler/merge/**
add gatk4/gatherbqsr (#1130) * nf-core modules create * add module files * indent * remove templte code * manually revert pytest changes from tools * manually revert pytest changes from tools * add include statement back in Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-12-08 22:43:36 +00:00
cooler/zoomify:
- modules/cooler/zoomify/**
- tests/software/cooler/zoomify/**
add csvtk/concat module (#785) * add csvtk/concat module * Update modules/csvtk/concat/main.nf Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> * allow alternate delimiters * Update main.nf * Update modules/csvtk/concat/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/csvtk/concat/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/csvtk/concat/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/csvtk/concat/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/csvtk/concat/main.nf * Apply suggestions from code review Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 20:48:47 +00:00
csvtk/concat:
- modules/csvtk/concat/**
- tests/modules/csvtk/concat/**
Added new module csvtk/split (#1014) * added module csvtk/split * removed todo statement * adjusted meta map names * changed tests to use generic input files * added module in pytest * updated test-data paths * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 18:29:55 +00:00
csvtk/split:
- modules/csvtk/split/**
- tests/modules/csvtk/split/**
Add custom/dumpsoftwareversions modules for nf-core pipeline template (#761) * Add custom/dumpsoftwareversions modules for nf-core pipeline template * Remove md5sums due to differing NF versions
2021-09-29 13:27:00 +00:00
custom/dumpsoftwareversions:
- modules/custom/dumpsoftwareversions/**
- tests/modules/custom/dumpsoftwareversions/**
Add module get_chrom_sizes (#1063) * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * init getchromsizes * add tests for getchromsizes * Included meta.yml * removed whitespace * Moved getchromsizes to custom folder * Update modules/custom/getchromsizes/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Svyatoslav Sidorov <svet.sidorov@gmail.com> Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com> Co-authored-by: Tamara Hodgetts <hodgett@crick.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 19:22:12 +00:00
custom/getchromsizes:
- modules/custom/getchromsizes/**
- tests/modules/custom/getchromsizes/**
refactor: rename module
2022-05-11 15:32:50 +00:00
custom/sratoolsncbisettings:
- modules/custom/sratoolsncbisettings/**
- tests/modules/custom/sratoolsncbisettings/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
cutadapt:
- modules/cutadapt/**
- tests/modules/cutadapt/**
damageprofiler:
- modules/damageprofiler/**
- tests/modules/damageprofiler/**
Add new module: Das Tool (#1004) * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs/outpus * remove trailing whitespace * compressing and removing not reproducible md5sums * follow symlinks while decompressing * add dastool/scaffolds2bin * add dastool * remove non reproducible md5sum check for compressed files * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * split tests * export env variable * remove metabat2 from PR * fix linting errors * remove traling whitespace * Update modules/metabat2/jgisummarizebamcontigdepths/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * answer PR comments and switch to bgzip * PR review updates * update from PR review * update test files * add bacillus fragilis alignments * switch tests to bacillus fragilis * add string check * update test string * add pr comment answer * last fixes for PR review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-19 07:33:29 +00:00
dastool/dastool:
- modules/dastool/dastool/**
- tests/modules/dastool/dastool/**
Update DASTool to 1.1.4 (#1471) * fix: remove left-over unnecessary code * Update DASTool * Fix tests * Fix test.ymls * Fix container build version * Make tests less strict to account for variability * Apply suggestions from code review Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Add missing description Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-04-01 09:33:07 +00:00
dastool/fastatocontig2bin:
- modules/dastool/fastatocontig2bin/**
- tests/modules/dastool/fastatocontig2bin/**
Add new module: Das Tool (#1004) * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs/outpus * remove trailing whitespace * compressing and removing not reproducible md5sums * follow symlinks while decompressing * add dastool/scaffolds2bin * add dastool * remove non reproducible md5sum check for compressed files * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * split tests * export env variable * remove metabat2 from PR * fix linting errors * remove traling whitespace * Update modules/metabat2/jgisummarizebamcontigdepths/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * answer PR comments and switch to bgzip * PR review updates * update from PR review * update test files * add bacillus fragilis alignments * switch tests to bacillus fragilis * add string check * update test string * add pr comment answer * last fixes for PR review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-19 07:33:29 +00:00
dastool/scaffolds2bin:
- modules/dastool/scaffolds2bin/**
- tests/modules/dastool/scaffolds2bin/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
Add module: `dedup` (#907) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add dedup (tests and version not working) * Fix dedup and tests Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-28 10:10:21 +00:00
dedup:
- modules/dedup/**
- tests/modules/dedup/**
Add `deeparg` (#1234) * Add deeparg download data * Tweak downloaddata test.yml * Add deeparg tests * Apply suggestions from code review * Fix output file paths in test * Fix tests again md5sum to string
2022-01-26 14:19:16 +00:00
deeparg/downloaddata:
- modules/deeparg/downloaddata/**
- tests/modules/deeparg/downloaddata/**
deeparg/predict:
- modules/deeparg/predict/**
- tests/modules/deeparg/predict/**
Add deeptools bamcoverage (#1316) * Add deeptools bamcoverage * remove todo string * Add in when * fix c&p version format error * Fix md5sums Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-18 08:35:41 +00:00
deeptools/bamcoverage:
- modules/deeptools/bamcoverage/**
- tests/modules/deeptools/bamcoverage/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
deeptools/computematrix:
- modules/deeptools/computematrix/**
- tests/modules/deeptools/computematrix/**
deeptools/plotfingerprint:
- modules/deeptools/plotfingerprint/**
- tests/modules/deeptools/plotfingerprint/**
deeptools/plotheatmap:
- modules/deeptools/plotheatmap/**
- tests/modules/deeptools/plotheatmap/**
deeptools/plotprofile:
- modules/deeptools/plotprofile/**
- tests/modules/deeptools/plotprofile/**
module: deepvariant (#572) * Add stubs for deepvariant [ci skip] * Update the stubs for deepvariant [ci skip] * functional with google docker image * cleanup * consume docker container within singularity executor * update the meta.yml file and ask for review * tweak the input channel shape and test data * tweak input data [ci skip] * update for the new syntax * remove the functions and rename meta vars * Update the arguments mechanism * update chr, region and checksum Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-01-17 10:25:36 +00:00
deepvariant:
- modules/deepvariant/**
- tests/modules/deepvariant/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
delly/call:
- modules/delly/call/**
- tests/modules/delly/call/**
Bbmap index (#683) BBMap index module
2021-09-03 07:28:28 +00:00
Diamond (#710) * Added diamond * minor tweaks & yml fix * Fixed spacing issues due to failing lint * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-23 08:13:04 +00:00
diamond/blastp:
- modules/diamond/blastp/**
- tests/modules/diamond/blastp/**
Add custom/dumpsoftwareversions modules for nf-core pipeline template (#761) * Add custom/dumpsoftwareversions modules for nf-core pipeline template * Remove md5sums due to differing NF versions
2021-09-29 13:27:00 +00:00
diamond/blastx:
- modules/diamond/blastx/**
- tests/modules/diamond/blastx/**
Diamond (#710) * Added diamond * minor tweaks & yml fix * Fixed spacing issues due to failing lint * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-23 08:13:04 +00:00
diamond/makedb:
- modules/diamond/makedb/**
- tests/modules/diamond/makedb/**
Dragmap (#1108) * feat(dragmap): Add initial hastable module * feat(dragmap): Add initial align module * test(dragmap): Remove md5sum Forgot sam files have a header. Might pipe this through samtools. * build(dragmap): Add mulled container * chore(dragmap): Update prefix * feat(dragmap): Output a bam file * feat(dragmap): Add log files * Update modules/dragmap/align/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-12-06 08:56:41 +00:00
dragmap/align:
- modules/dragmap/align/**
- tests/modules/dragmap/align/**
dragmap/hashtable:
- modules/dragmap/hashtable/**
- tests/modules/dragmap/hashtable/**
add module for dragonflye (#633) * add module for dragonflye * fix tests for dragonflye * Update test.yml * Update meta.yml * Update main.nf * Update main.nf * Update modules/dragonflye/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-16 09:51:30 +00:00
dragonflye:
- modules/dragonflye/**
- tests/modules/dragonflye/**
Add dsh-bio export-segments module (#631) Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-17 13:53:41 +00:00
dshbio/exportsegments:
- modules/dshbio/exportsegments/**
- tests/modules/dshbio/exportsegments/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
dshbio/filterbed:
- modules/dshbio/filterbed/**
- tests/modules/dshbio/filterbed/**
dshbio/filtergff3:
- modules/dshbio/filtergff3/**
- tests/modules/dshbio/filtergff3/**
dshbio/splitbed:
- modules/dshbio/splitbed/**
- tests/modules/dshbio/splitbed/**
dshbio/splitgff3:
- modules/dshbio/splitgff3/**
- tests/modules/dshbio/splitgff3/**
add ectyper module (#948) * add ectyper module * fix-lint * try zcat * Update main.nf * fix lint * Update main.nf * Apply suggestions from code review Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com> * Update main.nf * pass lint * Update main.nf * fix lint Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-21 12:14:02 +00:00
ectyper:
- modules/ectyper/**
- tests/modules/ectyper/**
New module: elprep filter (#1524) * first commit * syntax fix * fix input * output sam during test for md5sum * replace md5sum with contains * add new test data, add extra in/outputs * cli fixes * fix outputs * Update modules/elprep/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/elprep/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/elprep/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix suggestions by @jfy133 * Bit more verbose explanation for bool vals * define variables * fix prettier Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 09:08:03 +00:00
elprep/filter:
- modules/elprep/filter/**
- tests/modules/elprep/filter/**
first commit
2022-04-13 10:51:17 +00:00
elprep/merge:
- modules/elprep/merge/**
- tests/modules/elprep/merge/**
Tool/elprep split (#1533) * tool: elprep split * fixes for testing * fix tests * fix test outputs * create test-yaml * fix suggestions by @jfy133 Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 08:20:05 +00:00
elprep/split:
- modules/elprep/split/**
- tests/modules/elprep/split/**
add emmtyper module (#1028) Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 19:43:15 +00:00
emmtyper:
- modules/emmtyper/**
- tests/modules/emmtyper/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
ensemblvep:
- modules/ensemblvep/**
- tests/modules/ensemblvep/**
Add ENTREZDIRECT/ESUMMARY (#1833) * first commit * entrezdirect/esummary fixed version definition * resolved suggestion * updated main.nf * changed output definition * output: XML file * output definition: XML file * updated XML format in tests * updated test file * version: esummary instead of entrezdirect * output file pattern: *.esummary.xml * updated test file * updated versions * restored versions stdout * updated test file * changed xml_esummary pattern * changed entrezdirect to esummary version * updated test file * Update modules/entrezdirect/esummary/meta.yml changed output file pattern: "*.xml" Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/meta.yml updated keywords Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf Output file pattern: *.xml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf Output file pattern: *.xml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf database as separate input channel Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * removed blank spaces in input definition * database as separate channel * conditional script for stdin * updated input definition * entrez-direct version:16.2_1 * all input channels are separate * ignore stderr, catch xml stdout * removed blank lines * added ids file input * updated test * conditional script for input * removed bad definition of input file * updated test file * Update modules/entrezdirect/esummary/main.nf changed input definition: ui, uids_file Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/meta.yml added uids_file description Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * input: uid or uids_file * updated input * added uids_file to input * input file as optional input * input file as optional input in each test * new conditional script * unpdated test file * single input definition * added error messages * updated test * removed cat from command output * Update modules/entrezdirect/esummary/main.nf added comment on use of grep in output Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added comment * removed blank spaces * input file: empty list * input file: empty list * removed comment at wrong position * optional file defined as empty list * updated successful test * Apply suggestions from code review Accepted suggestions. Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * Update modules/entrezdirect/esummary/main.nf Fixed comment. Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * Update modules/entrezdirect/esummary/main.nf Updated grep in output file. Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * added tail -n+3 before output * updated successful test Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
2022-07-13 17:26:58 +00:00
entrezdirect/esummary:
- modules/entrezdirect/esummary/**
- tests/modules/entrezdirect/esummary/**
Expansionhunter (#666) Please enter the commit message for your changes. Lines starting * adds expansionhunter module Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-08-16 15:47:42 +00:00
expansionhunter:
- modules/expansionhunter/**
- tests/modules/expansionhunter/**
Faqcs (#1339) * Initial module creation * Update test.yml * Update test.yml * Update test.yml * Update meta.yml Co-authored-by: Cipriano <rrn8@cdc.gov> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-23 15:30:22 +00:00
faqcs:
- modules/faqcs/**
- tests/modules/faqcs/**
new module fargene (#1068) * new module fargene * Update main.nf * Update modules/fargene/main.nf * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 16:42:48 +00:00
fargene:
- modules/fargene/**
- tests/modules/fargene/**
module fastani (#695) * initiate agrvate module * remove todos [ci skip] * initiate fastani draft [ci skip] * clean stubs [ci skip] * interim commit [ci skip] * accomodate the batch/per-sample processing [ci skip] * use the meta map [ci skip] * run first test [ci skip] * remove extra spaces [ci skip] * change output file name [ci skip] * update the expected output [ci skip] * update the files used for test [ci skip] * fix typo [ci skip] * test passing [ci skip] * update the description * remove extra files * accomodate CR suggestions [ci skip] Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * accomodate CR suggestions [ci skip] Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * accomodate CR suggestions [ci skip] Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * use meta map for batch analysis * fix the tests * rely upon tuples * Apply suggestions from code review * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-21 19:20:26 +00:00
fastani:
- modules/fastani/**
- tests/modules/fastani/**
FastK/fastK (#1739) * Add FastK/FastK * Add ktab and prof outputs * Add the hidden files necessary for the optional files * Update image * Apply suggestions from code review Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-06-14 11:39:52 +00:00
fastk/fastk:
- modules/fastk/fastk/**
- tests/modules/fastk/fastk/**
Add FastK/Histex (#1776)
2022-06-14 14:30:37 +00:00
fastk/histex:
- modules/fastk/histex/**
- tests/modules/fastk/histex/**
Add FastK/Merge (#1828) * Add FastK/Merge * Update modules/fastk/merge/main.nf * Update modules/fastk/merge/meta.yml Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2022-06-29 16:04:36 +00:00
fastk/merge:
- modules/fastk/merge/**
- tests/modules/fastk/merge/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
fastp:
- modules/fastp/**
- tests/modules/fastp/**
fastqc:
- modules/fastqc/**
- tests/modules/fastqc/**
add module for fastq-scan (#935) * add module for fastq-scan * change fastq to reads * remove uncompressed support Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 14:41:36 +00:00
fastqscan:
- modules/fastqscan/**
- tests/modules/fastqscan/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
fasttree:
- modules/fasttree/**
- tests/modules/fasttree/**
Add ffq module (#1842)
2022-07-01 06:59:13 +00:00
ffq:
- modules/ffq/**
- tests/modules/ffq/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
fgbio/callmolecularconsensusreads:
- modules/fgbio/callmolecularconsensusreads/**
- tests/modules/fgbio/callmolecularconsensusreads/**
Rewritten module fgbio/fastqtobam (#916) * added template for fastqtobam * porting old code into new template * update with missing getprocessname function * test completed - updating all * fixed linting issues * improved reading Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-10-27 17:06:06 +00:00
fgbio/fastqtobam:
- modules/fgbio/fastqtobam/**
- tests/modules/fgbio/fastqtobam/**
Fgbio group reads by umi (#952) * adding template for module groupreadsbyumi * update modules with code * strategy is required argument so moving it to input rather than options.args * tests successful committing yml * added meta to output Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-29 12:00:54 +00:00
fgbio/groupreadsbyumi:
- modules/fgbio/groupreadsbyumi/**
- tests/modules/fgbio/groupreadsbyumi/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
fgbio/sortbam:
- modules/fgbio/sortbam/**
- tests/modules/fgbio/sortbam/**
add filtlong (#919)
2021-10-27 15:00:11 +00:00
filtlong:
- modules/filtlong/**
- tests/modules/filtlong/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
flash:
- modules/flash/**
- tests/modules/flash/**
Add new module: Flye (#1164) * changing mv by gzip * changing mv by gzip * first module creation * add test.yml * add flye to pyestes_modules.yml * update flye module * delete functions.nf * generate test.yml * fix contains from test.yml * test file assembly_info.txt with regex * check that file contains at least contig_1 * fix typo in contains * update version * split fastq file for raw runs * use asm-coverage to reduce memory usage * fix module name error * add genome-size * decrease coverage * change test data for raw runs * add coverage and genome size * Apply comments from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * after many trys, add a stub run * remove md5sum for stub run * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix review comments * Apply suggestions from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * no hardcoded version in stub run * Update modules/flye/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-06-30 20:45:55 +00:00
flye:
- modules/flye/**
- tests/modules/flye/**
Merge freebayes subtools (#1015) * feat: merge freebayes subtools * fix: typo * assess comments from review * fix: path to module
2021-11-03 10:22:06 +00:00
freebayes:
- modules/freebayes/**
- tests/modules/freebayes/**
New module: freebayes (#818) * add pydamage module Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-20 13:19:31 +00:00
fixed pytest_modules.yml
2022-05-24 23:19:38 +00:00
gamma/gamma:
- modules/gamma/gamma/**
- tests/modules/gamma/gamma/**
new module: GAMMA (#1532) * initial version of gamma module * remove trailing whitespace * prettier fix * hardcode version number * Update modules/gamma/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/gamma/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/gamma/meta.yml Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * update meta and prettier * add whitespaces * add fasta output and tests Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-23 14:12:06 +00:00
Add gatk/indelrealigner
2022-05-30 19:12:21 +00:00
gatk/indelrealigner:
- modules/gatk/indelrealigner/**
- tests/modules/gatk/indelrealigner/**
Skeleton
2022-05-31 18:13:48 +00:00
gatk/realignertargetcreator:
- modules/gatk/realignertargetcreator/**
- tests/modules/gatk/realignertargetcreator/**
Star work on GATK UG
2022-06-02 19:11:17 +00:00
gatk/unifiedgenotyper:
- modules/gatk/unifiedgenotyper/**
- tests/modules/gatk/unifiedgenotyper/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/applybqsr:
- modules/gatk4/applybqsr/**
- tests/modules/gatk4/applybqsr/**
update gatk4 yml for spark (#1538)
2022-04-19 14:51:59 +00:00
gatk4/applybqsrspark:
- modules/gatk4/applybqsrspark/**
- tests/modules/gatk4/applybqsrspark/**
Add applyvqsr (#1101) * initial commit to setup branch * workflow finished * Update nextflow.config * tumour to tumor, getpileup passed as nomral and tumor * paired_somatic renamed to tumor_normal_somatic * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * updated index names in meta.yml * changed index file names in main script and test * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Apply suggestions from code review * fixed bug from changes * Apply suggestions from code review * modified yml to allow new subworkflow testing * Update test.yml * Update test.yml * add applyvqsr * added memory options, new test data used * Update main.nf * Update main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-12-16 08:44:50 +00:00
gatk4/applyvqsr:
- modules/gatk4/applyvqsr/**
- tests/modules/gatk4/applyvqsr/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/baserecalibrator:
- modules/gatk4/baserecalibrator/**
- tests/modules/gatk4/baserecalibrator/**
update gatk4 yml for spark (#1538)
2022-04-19 14:51:59 +00:00
gatk4/baserecalibratorspark:
- modules/gatk4/baserecalibratorspark/**
- tests/modules/gatk4/baserecalibratorspark/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/bedtointervallist:
- modules/gatk4/bedtointervallist/**
- tests/modules/gatk4/bedtointervallist/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
gatk4/calculatecontamination:
new module: gatk4/calculatecontamination (#778) * initiated files for calculate contamination * pushing local repo to remote * created script, filled in meta yml, created tests and test yml. local checks passing, needs repo side test data * added option and tests for outputting optional segmentation file * saving for test push * versions updated, test data added * Update main.nf * fixed versions info, should report correctly now * small update to main.nf outputs formatting * Apply suggestions from code review * Update test_data.config * Apply suggestions from code review Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:52:00 +00:00
- modules/gatk4/calculatecontamination/**
- tests/modules/gatk4/calculatecontamination/**
added the calibratedragstrmodel module
2022-06-02 11:17:06 +00:00
gatk4/calibratedragstrmodel:
- modules/gatk4/calibratedragstrmodel/**
- tests/modules/gatk4/calibratedragstrmodel/**
update pytest
2022-05-17 17:11:05 +00:00
gatk4/cnnscorevariants:
- modules/gatk4/cnnscorevariants/**
- tests/modules/gatk4/cnnscorevariants/**
Gatk4 combinegvcfs (#1342) * add gatk4/combinegvcfs module * update gatk4/combinegvcfs * loop to create a string adding -V to each vcf file * add contains for variable md5 * rm whitespace * meta in output * fix indentations * fix indentations * move tmpdir to args and update conda version Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-23 15:29:29 +00:00
gatk4/combinegvcfs:
- modules/gatk4/combinegvcfs/**
- tests/modules/gatk4/combinegvcfs/**
added gatk4/composestrtablefile
2022-05-31 14:08:13 +00:00
gatk4/composestrtablefile:
- modules/gatk4/composestrtablefile/**
- tests/modules/gatk4/composestrtablefile/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/createsequencedictionary:
- modules/gatk4/createsequencedictionary/**
- tests/modules/gatk4/createsequencedictionary/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
gatk4/createsomaticpanelofnormals:
Createsomaticpanelofnormals (#859) * files created for createsompon, script written, meta written, still needs tests * updated to 2.0.0 method input, however this requires a genomicsDB input now * script finished, meta yaml updated. Tests working locally, test yaml made, needs genomicsdb example on nf-core to run repository tests * versions updated, issue with test data not able to download directory * updated tests to include repo-side data * Apply suggestions from code review * Update modules/gatk4/createsomaticpanelofnormals/main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 18:30:14 +00:00
- modules/gatk4/createsomaticpanelofnormals/**
- tests/modules/gatk4/createsomaticpanelofnormals/**
Add gatk4/estimatelibrarycomplexity (#965) * Add gatk4/estimatelibrarycomplxity * forgot to add yml * Fix placeholder
2021-10-28 15:49:27 +00:00
gatk4/estimatelibrarycomplexity:
- modules/gatk4/estimatelibrarycomplexity/**
- tests/modules/gatk4/estimatelibrarycomplexity/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/fastqtosam:
- modules/gatk4/fastqtosam/**
- tests/modules/gatk4/fastqtosam/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
gatk4/filtermutectcalls:
Filtermutectcalls (#796) * first commit with files for filtermutectcalls initialised * found missing test file that needs to be resolved * saving config changes * fixing pytest_module conflict * finished module, just needs repository side tests added * test data added, versions file updated * modified to emit correct versions file * Update main.nf * Update test_data.config * updated test script * fixed main.nf * Update main.nf * Update main.nf * removed whitespace from test script * Update test_data.config * Update .gitignore * Update test_data.config * tests changed to new names, main script edited to match comments on learnreads pr * Update meta.yml * Apply suggestions from code review * Update main.nf * Apply suggestions from code review * Apply suggestions from code review * Update main.nf * Update main.nf * Update main.nf * Update main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 17:45:19 +00:00
- modules/gatk4/filtermutectcalls/**
- tests/modules/gatk4/filtermutectcalls/**
add filter variant tranches
2022-05-17 21:01:24 +00:00
gatk4/filtervarianttranches:
- modules/gatk4/filtervarianttranches/**
- tests/modules/gatk4/filtervarianttranches/**
add gatk4/gatherbqsr (#1130) * nf-core modules create * add module files * indent * remove templte code * manually revert pytest changes from tools * manually revert pytest changes from tools * add include statement back in Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-12-08 22:43:36 +00:00
gatk4/gatherbqsrreports:
- modules/gatk4/gatherbqsrreports/**
- tests/modules/gatk4/gatherbqsrreports/**
Add gatherpileupsummaries (#1311) * Add gatherpileupsummaries * fix checksum * Update modules/gatk4/gatherpileupsummaries/main.nf * Add in when
2022-02-17 14:05:21 +00:00
gatk4/gatherpileupsummaries:
- modules/gatk4/gatherpileupsummaries/**
- tests/modules/gatk4/gatherpileupsummaries/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
gatk4/genomicsdbimport:
add seqsero2 module (#1016) * add seqsero2 module * correct lint errors * Update modules/seqsero2/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * set output directory Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-04 07:49:30 +00:00
- modules/gatk4/genomicsdbimport/**
- tests/modules/gatk4/genomicsdbimport/**
New modules added: issues #200 and #310 (#884) * New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
gatk4/genotypegvcfs:
- modules/gatk4/genotypegvcfs/**
- tests/modules/gatk4/genotypegvcfs/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
gatk4/getpileupsummaries:
Getpileupsummaries (#689) * first commit, added template files for new module * created getpileupsummaries script, tests and both yml files * fixed typo in meta.yml * Update modules/gatk4/getpileupsummaries/meta.yml changed gz_tbi to gz.tbi as suggested Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2021-09-13 15:04:14 +00:00
- modules/gatk4/getpileupsummaries/**
- tests/modules/gatk4/getpileupsummaries/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/haplotypecaller:
- modules/gatk4/haplotypecaller/**
- tests/modules/gatk4/haplotypecaller/**
New modules added: issues #200 and #310 (#884) * New modules added: issues #200 and #310 * Update main.nf * Update meta.yml * Update tests/modules/gatk4/genotypegvcfs/main.nf * Apply suggestions from code review * Update main.nf * Updating tests for GenomicsDB input and adding the path for this test resource to test_data.config * Some minor changes on one of the test files I forgot to include Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: GCJMackenzie <43276267+GCJMackenzie@users.noreply.github.com>
2021-11-15 15:43:06 +00:00
gatk4/indexfeaturefile:
- modules/gatk4/indexfeaturefile/**
- tests/modules/gatk4/indexfeaturefile/**
intervallisttobed (#1312) * intervallisttobed * correct md5sum
2022-02-17 15:32:26 +00:00
gatk4/intervallisttobed:
- modules/gatk4/intervallisttobed/**
- tests/modules/gatk4/intervallisttobed/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/intervallisttools:
- modules/gatk4/intervallisttools/**
- tests/modules/gatk4/intervallisttools/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
gatk4/learnreadorientationmodel:
Learnreadorientationmodel (#794) * files for learnreadorientationmodel initialised for first commit * finished scripts and yml files. test working locally but needs an f1r2 test data on nf-core before it can be submitted * updated test data location * versions file updated, test data added * updated versions file, edited test file * small formatting update to main.nf * Update main.nf * Update test_data.config * updated tests main.nf * Update test_data.config * Apply suggestions from code review * Update modules/gatk4/learnreadorientationmodel/main.nf * Update modules/gatk4/learnreadorientationmodel/meta.yml * fixed tests failing Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-07 12:55:06 +00:00
- modules/gatk4/learnreadorientationmodel/**
- tests/modules/gatk4/learnreadorientationmodel/**
Add module: gatk4/leftalignandtrimvariants (#1808) * Added: gatk4/leftalignandtrimvariants Additions: - GATK4/LeftAlignAndTrimVariants module - Use sars-ncov2 test data as this normalises a larger INDEL correctly. Fixes #1801 * fixup: Added index to output spec * fixup: Pattern of tbi output corrected to 'tbi' * gatk4/leftalignandtrimvariants: Added intervals Changes: - gatk4/leftalignandtrimvariants now supports optional interval as BED file - Tests added with and without interval. Not test BED file excludes all variants so no variants are actually normalised. Fixes #1801 * fixup: leftalignandtrimvariants vcf->tbi fix * fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
2022-06-28 08:44:08 +00:00
gatk4/leftalignandtrimvariants:
- modules/gatk4/leftalignandtrimvariants/**
- tests/modules/gatk4/leftalignandtrimvariants/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/markduplicates:
- modules/gatk4/markduplicates/**
- tests/modules/gatk4/markduplicates/**
update gatk4 yml for spark (#1538)
2022-04-19 14:51:59 +00:00
gatk4/markduplicatesspark:
- modules/gatk4/markduplicatesspark/**
- tests/modules/gatk4/markduplicatesspark/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/mergebamalignment:
- modules/gatk4/mergebamalignment/**
- tests/modules/gatk4/mergebamalignment/**
add mergemutectstats (#1314) * add mergemutectstats * correct md5sum * Update modules/gatk4/mergemutectstats/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-18 08:38:55 +00:00
gatk4/mergemutectstats:
- modules/gatk4/mergemutectstats/**
- tests/modules/gatk4/mergemutectstats/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/mergevcfs:
- modules/gatk4/mergevcfs/**
- tests/modules/gatk4/mergevcfs/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
gatk4/mutect2:
Mutect2 (#682) * mutect2 files added, first draft of module code entered * removing comment from main.nf * removing comment from main.nf * test added, commit made before editing yaml * tests added, still needs final check and info/comments added * gatk4 version changed to gatk4=4.2.0.0 * multiple sample support added, information added to module yaml file * Update meta.yml fixed linting error * add keywords to meta.yml * Corrections made to meta.yml * removed whitespace from meta.yml Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-09-13 15:16:23 +00:00
- modules/gatk4/mutect2/**
- tests/modules/gatk4/mutect2/**
new module gatk4/reblockgvcf
2022-06-09 12:56:55 +00:00
gatk4/reblockgvcf:
- modules/gatk4/reblockgvcf/**
- tests/modules/gatk4/reblockgvcf/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/revertsam:
- modules/gatk4/revertsam/**
- tests/modules/gatk4/revertsam/**
gatk4/samtofastq:
- modules/gatk4/samtofastq/**
- tests/modules/gatk4/samtofastq/**
Gatk4 selectvariants (#1346) * initial commit * tested Co-authored-by: Cipriano <rrn8@cdc.gov> Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-24 08:51:48 +00:00
gatk4/selectvariants:
- modules/gatk4/selectvariants/**
- tests/modules/gatk4/selectvariants/**
added gatk4/splitintervals
2022-05-13 11:46:34 +00:00
gatk4/splitintervals:
- modules/gatk4/splitintervals/**
- tests/modules/gatk4/splitintervals/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gatk4/splitncigarreads:
- modules/gatk4/splitncigarreads/**
- tests/modules/gatk4/splitncigarreads/**
gatk4/variantfiltration:
- modules/gatk4/variantfiltration/**
- tests/modules/gatk4/variantfiltration/**
add module: Variantrecalibrator (#1088) * committing to pull updated nf-core files * saving changes to checout other branch * committing progress so far, difficulty with test data * uploading to be used as draft PR * fix linting error in meta.yml * attempt to group reference inputs together * updated input format for resources * meta.yml updated with new resource names * added output channel for recal index * module only takes single vcf file input now * committing to checkout * update to new syntax, remove indel test for now * updated to use memory options and new test data * Update modules/gatk4/variantrecalibrator/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update main.nf * Update modules/gatk4/variantrecalibrator/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * remove duplicate test keys from test_data.config Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-12-16 10:54:49 +00:00
gatk4/variantrecalibrator:
- modules/gatk4/variantrecalibrator/**
- tests/modules/gatk4/variantrecalibrator/**
Add gecco/run module (#1790) * Add gecco/run module * Fix container URLs * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-06-22 11:43:45 +00:00
gecco/run:
- modules/gecco/run/**
- tests/modules/gecco/run/**
Add GeneScopeFK (#1781)
2022-06-14 18:49:06 +00:00
genescopefk:
- modules/genescopefk/**
- tests/modules/genescopefk/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
genmap/index:
- modules/genmap/index/**
- tests/modules/genmap/index/**
genmap/mappability:
- modules/genmap/mappability/**
- tests/modules/genmap/mappability/**
create genomescope2 module
2022-05-09 15:09:15 +00:00
genomescope2:
- modules/genomescope2/**
- tests/modules/genomescope2/**
New module: genrich (#877) * Add genrich module * Rearrange genrich module from genrich/genrich to genrich * Remove copy/paste code * Fix meta.yml * Implement save_duplicates independently of -r opt
2021-10-22 10:22:02 +00:00
genrich:
- modules/genrich/**
- tests/modules/genrich/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gffread:
- modules/gffread/**
- tests/modules/gffread/**
Add glnexus (#729) * Add glnexus * Fix lint error * Refactor * Suggested changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-22 12:31:01 +00:00
glnexus:
- modules/glnexus/**
- tests/modules/glnexus/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
graphmap2/align:
- modules/graphmap2/align/**
- tests/modules/graphmap2/align/**
graphmap2/index:
- modules/graphmap2/index/**
- tests/modules/graphmap2/index/**
New module: `gstama/collapse` (#809) * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add gd-tama module * 🐛 FIX (TEMP): Update singularity container address * 📦 NEW: Add bamtools module * 📦 NEW: Rewrite and rename module (gstama => gstama/collapse) * 👌 IMPROVE: ignore test data * 👌 IMPROVE: Remove junk files * 👌 IMPROVE: Update output * 👌 IMPROVE: Add channel for publishing tama's metadata outputs * 👌 IMPROVE: Update process label * 🐛 FIX: Use depot.galxyproject.org url for singularity * 👌 IMPROVE: autoselect running mode * 🐛 FIX: correct gstama collapse bash test * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update tama package and label * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update test * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add gd-tama module * 🐛 FIX (TEMP): Update singularity container address * 📦 NEW: Add bamtools module * 📦 NEW: Rewrite and rename module (gstama => gstama/collapse) * 👌 IMPROVE: ignore test data * 👌 IMPROVE: Update output * 👌 IMPROVE: Add channel for publishing tama's metadata outputs * 👌 IMPROVE: Update process label * 🐛 FIX: Use depot.galxyproject.org url for singularity * 👌 IMPROVE: autoselect running mode * 🐛 FIX: correct gstama collapse bash test * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update tama package and label * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update test * 👌 IMPROVE: delete unnecessary files * 👌 IMPROVE: Update + clean - Remove unnecessary files - Update to new versions.yml file - Better output channels * 👌 IMPROVE: Update meta.yml and output channels * 👌 IMPROVE: Remove useless files * 👌 IMPROVE: Remove automatic MODE setup * 👌 IMPROVE: Applied @jfy133 code modification suggestions * Update modules/gstama/collapse/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 🐛 FIX: Add missing fasta option in meta.yml * 🐛 FIX: Fix typo * 🐛 FIX: Update package version * Update main.nf * Update meta.yml * Update modules/gstama/collapse/meta.yml * Apply suggestions from code review * Update tests/modules/gstama/collapse/main.nf * Update main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 17:55:28 +00:00
gstama/collapse:
- modules/gstama/collapse/**
- tests/modules/gstama/collapse/**
New module: `gstama/merge` (#813) * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: ignore test data * 👌 IMPROVE : add test bed files * 📦 NEW: Add gstama/merge module * 🐛 FIX: Change process label * 👌 IMPROVE: do not merge empty bed * 🐛 FIX: Change 0 lines files detection * 🐛 FIX: replace spaces by tab * 🐛 FIX: Remove tuple for report channel and add version output channel * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Update test * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fix Typos * 👌 IMPROVE: Updates + clean code - Update to last versions.yml file - Better output channels - Update meta.yml * 👌 IMPROVE: Correct typo * 👌 IMPROVE: Remove included filelist creation and add an input channel * 🐛 FIX: Correct typo * 👌 IMPROVE: Add filelist file * 🐛 FIX: tama_merge.py emit a version number * Update modules/gstama/merge/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * 👌 IMPROVE: Update meta.yml * Update main.nf * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-23 18:00:39 +00:00
gstama/merge:
- modules/gstama/merge/**
- tests/modules/gstama/merge/**
New Module: `gstama/polyacleanup` (#1468) * 📦 NEW: Add gstama/polyacleanup polyacleanup script remove remaining polyA tails from FLNC reads (Pacbio isoseq3) * 🐛 FIX: Prettier: replace simple quote by double quote * 🐛 FIX: Update TEMPLATE to nf-core 2.4 * 👌 IMPROVE: Compress outputs Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-03-31 13:11:51 +00:00
gstama/polyacleanup:
- modules/gstama/polyacleanup/**
- tests/modules/gstama/polyacleanup/**
Add gtdbtk/classifywf module (#765) * initial commit [ci skip] * reuse the modules code from nf-core/mag [ci skip] * add contextual information for the module [ci skip] * add stubs to avoid downloading db [ci skip] * trigger test * iterate on tests [ci skip] * itereate tests [ci skip] * add bins [ci skip] * fix stubs [ci skip] * interation on tests with stubs [ci skip] * use the existing pattern and fasta for input * accomodate the new version file format * use variable for the stub [ci skip] * update the versions file in meta.yml * Accomodate code review regarding publishDir function [ci skip] Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * remove extra newline * use bioconda channel * update the description for filtered file * Apply suggestions from code review * Update main.nf * Update main.nf * Update modules/gtdbtk/classifywf/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 20:23:01 +00:00
gtdbtk/classifywf:
- modules/gtdbtk/classifywf/**
- tests/modules/gtdbtk/classifywf/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gubbins:
- modules/gubbins/**
- tests/modules/gubbins/**
New module: `gunc run` (+ `gunc downloaddb`) (#880) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add GUNC download_db and run commands * Bump with version without zgrep * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * Harshil formatting * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-11-03 16:01:23 +00:00
gunc/downloaddb:
- modules/gunc/downloaddb/**
- tests/modules/gunc/downloaddb/**
gunc/run:
- modules/gunc/run/**
- tests/modules/gunc/run/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
gunzip:
- modules/gunzip/**
- tests/modules/gunzip/**
Add `hamronization/deeparg` (#1364) * fix: remove left-over unnecessary code * Add hamronizer/deeparg * Add when condition * Apply suggestions from code review * Update modules/hamronization/deeparg/meta.yml
2022-03-02 12:04:22 +00:00
hamronization/deeparg:
- modules/hamronization/deeparg/**
- tests/modules/hamronization/deeparg/**
new module hamronization/rgi (#1844) * new module hamronization/rgi * remove comments * Update modules/hamronization/rgi/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-01 10:03:08 +00:00
hamronization/rgi:
- modules/hamronization/rgi/**
- tests/modules/hamronization/rgi/**
Add `hamronization/summarize` (#1366) * fix: remove left-over unnecessary code * Add hamronizer/deeparg * Add hamronisation/summarise * Update test.yml * Update modules/hamronization/summarize/meta.yml Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * line up outputs Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
2022-03-03 07:02:04 +00:00
hamronization/summarize:
- modules/hamronization/summarize/**
- tests/modules/hamronization/summarize/**
tests: add haplocheck tests
2022-05-13 10:42:34 +00:00
haplocheck:
- modules/haplocheck/**
- tests/modules/haplocheck/**
Changed the pytest location of happy
2022-05-04 13:40:34 +00:00
happy/happy:
- modules/happy/happy/**
- tests/modules/happy/happy/**
Added the module and some simple testing
2022-05-04 11:42:12 +00:00
Split the module into two parts
2022-05-04 13:29:48 +00:00
happy/prepy:
- modules/happy/prepy/**
- tests/modules/happy/prepy/**
add hicap module (#772) * add hicap module * add info on optional inputs * fix typo * Update meta.yml * Update main.nf * Update meta.yml * Update modules/hicap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/hicap/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 20:42:09 +00:00
hicap:
- modules/hicap/**
- tests/modules/hicap/**
Add hifiasm module (#596) * Add hifiasm module * Tidy up module * Add pacbio files to test_data.config
2021-07-20 20:50:22 +00:00
hifiasm:
- modules/hifiasm/**
- tests/modules/hifiasm/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
hisat2/align:
- modules/hisat2/align/**
- modules/hisat2/build/**
- modules/hisat2/extractsplicesites/**
- tests/modules/hisat2/align/**
hisat2/build:
- modules/hisat2/build/**
- modules/hisat2/extractsplicesites/**
- tests/modules/hisat2/build_test/**
hisat2/extractsplicesites:
- modules/hisat2/extractsplicesites/**
- tests/modules/hisat2/extractsplicesites/**
gccounter module for hmmcopy (#1003) * hmmcopy gccounter working * Update modules/hmmcopy/gccounter/main.nf Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com> * Update main.nf Changed version to 0.1.1 as the container says Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-02 09:59:25 +00:00
hmmcopy/gccounter:
- modules/hmmcopy/gccounter/**
- tests/modules/hmmcopy/gccounter/**
New subtool: hmmcopy/generatemap (#1168) * Initial structure * Working with local singularity image * Working generateMap.pl script * Remote not working bioconda * Working generateMap with biocontainer * Lint changes * Updated hmmcopy container version to be consistent * Fix failing test * Remove path to perl * No hardpath to script * Update main.nf Moved version outside of process, add support for zipped fasta file * Revert to not allowing gzip via pipe, as perl script can't cope Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
2021-12-15 15:57:42 +00:00
hmmcopy/generatemap:
- modules/hmmcopy/generatemap/**
- tests/modules/hmmcopy/generatemap/**
hmmcopy/mapCounter (#1175) * hmmcopy/mapCounter * update test * Remove bam tag * Remove /tmp/ path from test.yml * Update modules/hmmcopy/mapcounter/meta.yml Incorporate formatting changes Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/hmmcopy/mapcounter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/hmmcopy/mapcounter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-12-17 15:39:50 +00:00
hmmcopy/mapcounter:
- modules/hmmcopy/mapcounter/**
- tests/modules/hmmcopy/mapcounter/**
readcounter module for hmmcopy (#1001) * readcounter module for hmmcopy * Changed version number * Fix indentation * Update main.nf * Update modules/hmmcopy/readcounter/main.nf Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com> Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-11-02 11:01:13 +00:00
hmmcopy/readcounter:
- modules/hmmcopy/readcounter/**
- tests/modules/hmmcopy/readcounter/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
hmmer/hmmalign:
- modules/hmmer/hmmalign/**
- tests/modules/hmmer/hmmalign/**
feat: add hmmsearch module and tests (#1273) * feat: add hmmsearch module and tests * chore: set medium resource requirements * tests: look for correct output * fix: add when condition * Apply suggestions to meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * refactor: create gzip compressed output * docs: describe compressed in-/output Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-02-23 14:32:33 +00:00
hmmer/hmmsearch:
- modules/hmmer/hmmsearch/**
- tests/modules/hmmer/hmmsearch/**
modified: tests/config/pytest_modules.yml
2022-05-13 12:29:12 +00:00
hmtnote:
- modules/hmtnote/**
- tests/modules/hmtnote/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
homer/annotatepeaks:
- modules/homer/annotatepeaks/**
- tests/modules/homer/annotatepeaks/**
Homer Modules (#75) * feat(homer): Add initial makeTagDirectory * feat(homer): Add initial findPeaks module * feat(homer): Update with new options See 1d30e2c21affedc742680e8e04d60c6481d9cd11 * fix(homer): Correct findpeaks process name * fix(homer): Takes a bam file instead of bed * feat(homer): Add initial makeTagDirectory test * fix(homer): Hardcode genome and configureHomer I'd like to modularize configureHomer, but I need to figure out how exactly the genomes work. * fix(homer): bam => bed Bam requires samtools to be present, which it's not in this docker image * feat(homer): Add initial configureHomer script * ci(homer): Add initial test * test(homer): Reproducible configuration workaround - I can't run both tests(one file and two files) at the same time because it breaks - I can't copy the genome stuff from the configurehomer module because it's read only - So I can't make the makeTagDirectory module depend on configureHomer * test(homer): Add placeholder annotatepeaks The required inputs are necessarily required for all workflows from what I've used, but I'll need to look at the actual docs * test(homer): Add missing B.bed * test(homer): Rename two => groseq Then all of the various workflows that homer provides can be e2e tested * feat(homer): Add initial makeUCSCfile module * test(homer): Add start to makeUCSCfile testing * chore(homer): Add various cleanups * test(homer): Rewrite annotatepeaks Not passing yet * test(homer): Rewrite configurehomer * test(homer): Rewrite findpeaks Still failing * test(homer): Rewrite makeucscfile Not passing yet * test(homer): Rewrite maketagdirectory All homer modules now follow the new structure. Time to make them pass. * test(homer): Fix typo for workflow name * fix(homer): Use correct container * fix(homer): Accept fasta in maketagdirectory Apparently all of the homer stuff can just take any old fasta and you don't need to configure the genome ahead of time with configureHomer * test(homer): makeTagDirectory passes now * fix(homer): Update containers in makeucscfile * test(homer): Rewrite makeucscfile Takes input from maketagdirectory which is how the module should be used * fix(homer): Update makeUCSCFile bedgraph path * test(homer): Update makeucscfile expected output * fix(homer): Update containers in findpeaks * fix(homer): Change findpeaks args The user is just going to have to know what they're doing for now * test(homer): findPeaks rewrite with tagDir input * test(homer): Update expected files for findPeaks And bump filters * style: Appease editorconfig * ci: Remove old workflow * tests(homer): Add md5sums * test(homer): Add meta test * style(homer): Capitalize HOMER * docs(homer): Add maketagdirectory meta.yml * docs(homer): Add makeucscfile meta.yml * docs(homer): Add findpeaks meta.yml * test(homer): Update to new test data standards * chore: Remove stuff that got revived in the rebase * chore: software => modules * test(homer): Update tags * test(homer): Update annotatepeaks * ci: Fix uploading of artifacts GitHub actions doesn't like the / in the tags * test(homer): Remove annotate md5sum This is failing and breaking new tests * test(homer): Use bams instead of beds * test(homer): Fix meta maketagdirectory * test(homer): Fix input in all tests * test(homer): Move back to bed files Forgot samtools isn't present * chore(homer): Add TODOs for tests * test(homer): Add bed format arg * test(homer): Update md5sums * test(homer): Fix tags tsvs * style(homer): Appease nf-core linting * docs(homer): Be in line with what is in the main.nf file Co-authored-by: Kevin Menden <kevin.menden@live.com> Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-09-08 15:40:34 +00:00
homer/findpeaks:
- modules/homer/findpeaks/**
Homer/findpeaks improvements (#1436) * fix(homer): Update expected file path to improve caching * docs(homer): Update findpeaks * test(homer): Add maketagdirectory dependency Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-03-25 02:44:12 +00:00
- modules/homer/maketagdirectory/**
Homer Modules (#75) * feat(homer): Add initial makeTagDirectory * feat(homer): Add initial findPeaks module * feat(homer): Update with new options See 1d30e2c21affedc742680e8e04d60c6481d9cd11 * fix(homer): Correct findpeaks process name * fix(homer): Takes a bam file instead of bed * feat(homer): Add initial makeTagDirectory test * fix(homer): Hardcode genome and configureHomer I'd like to modularize configureHomer, but I need to figure out how exactly the genomes work. * fix(homer): bam => bed Bam requires samtools to be present, which it's not in this docker image * feat(homer): Add initial configureHomer script * ci(homer): Add initial test * test(homer): Reproducible configuration workaround - I can't run both tests(one file and two files) at the same time because it breaks - I can't copy the genome stuff from the configurehomer module because it's read only - So I can't make the makeTagDirectory module depend on configureHomer * test(homer): Add placeholder annotatepeaks The required inputs are necessarily required for all workflows from what I've used, but I'll need to look at the actual docs * test(homer): Add missing B.bed * test(homer): Rename two => groseq Then all of the various workflows that homer provides can be e2e tested * feat(homer): Add initial makeUCSCfile module * test(homer): Add start to makeUCSCfile testing * chore(homer): Add various cleanups * test(homer): Rewrite annotatepeaks Not passing yet * test(homer): Rewrite configurehomer * test(homer): Rewrite findpeaks Still failing * test(homer): Rewrite makeucscfile Not passing yet * test(homer): Rewrite maketagdirectory All homer modules now follow the new structure. Time to make them pass. * test(homer): Fix typo for workflow name * fix(homer): Use correct container * fix(homer): Accept fasta in maketagdirectory Apparently all of the homer stuff can just take any old fasta and you don't need to configure the genome ahead of time with configureHomer * test(homer): makeTagDirectory passes now * fix(homer): Update containers in makeucscfile * test(homer): Rewrite makeucscfile Takes input from maketagdirectory which is how the module should be used * fix(homer): Update makeUCSCFile bedgraph path * test(homer): Update makeucscfile expected output * fix(homer): Update containers in findpeaks * fix(homer): Change findpeaks args The user is just going to have to know what they're doing for now * test(homer): findPeaks rewrite with tagDir input * test(homer): Update expected files for findPeaks And bump filters * style: Appease editorconfig * ci: Remove old workflow * tests(homer): Add md5sums * test(homer): Add meta test * style(homer): Capitalize HOMER * docs(homer): Add maketagdirectory meta.yml * docs(homer): Add makeucscfile meta.yml * docs(homer): Add findpeaks meta.yml * test(homer): Update to new test data standards * chore: Remove stuff that got revived in the rebase * chore: software => modules * test(homer): Update tags * test(homer): Update annotatepeaks * ci: Fix uploading of artifacts GitHub actions doesn't like the / in the tags * test(homer): Remove annotate md5sum This is failing and breaking new tests * test(homer): Use bams instead of beds * test(homer): Fix meta maketagdirectory * test(homer): Fix input in all tests * test(homer): Move back to bed files Forgot samtools isn't present * chore(homer): Add TODOs for tests * test(homer): Add bed format arg * test(homer): Update md5sums * test(homer): Fix tags tsvs * style(homer): Appease nf-core linting * docs(homer): Be in line with what is in the main.nf file Co-authored-by: Kevin Menden <kevin.menden@live.com> Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-09-08 15:40:34 +00:00
- tests/modules/homer/findpeaks/**
homer/maketagdirectory:
- modules/homer/maketagdirectory/**
- tests/modules/homer/maketagdirectory/**
homer/makeucscfile:
- modules/homer/makeucscfile/**
- tests/modules/homer/makeucscfile/**
feat(homer): Add pos2bed module (#1435) * feat(homer): Add pos2bed module * test(homer): Pass bed format * test(homer): Add upstream dependencies to avoid regressions * Update modules/homer/pos2bed/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-03-25 13:29:36 +00:00
homer/pos2bed:
- modules/homer/pos2bed/**
- modules/homer/maketagdirectory/**
- modules/homer/findpeaks/**
- tests/modules/homer/pos2bed/**
add module for hpsuisero (#1331) * add module for hpsuisero * Update meta.yml * Update main.nf Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-28 00:58:35 +00:00
hpsuissero:
- modules/hpsuissero/**
- tests/modules/hpsuissero/**
New module: ichorCNA (#1182) * hmmcopy/mapCounter * update test * Remove bam tag * Remove /tmp/ path from test.yml * Update modules/hmmcopy/mapcounter/meta.yml Incorporate formatting changes Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/hmmcopy/mapcounter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/hmmcopy/mapcounter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * ichorCNA run * Add panel of normals code * Try and fix tests * Edit string detection in tests * Fix linting issues * Just failing END_VERSIONS * Fixed versions.yml * Added DOI * Optional name for file * Add when command * Updated when * Update modules/ichorcna/createpon/main.nf Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-02-11 15:56:13 +00:00
ichorcna/createpon:
- modules/ichorcna/createpon/**
- tests/modules/ichorcna/createpon/**
ichorcna/run:
- modules/ichorcna/run/**
- tests/modules/ichorcna/run/**
Add IDR module (#908) * Add IDR module * Add meta and implement main todos * Modifying idr tests * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update main.nf * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test with new file name Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-10-30 08:52:13 +00:00
idr:
- modules/idr/**
- tests/modules/idr/**
Add `leehom` module (#1052) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add leeHom module * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 14:26:06 +00:00
imputeme/vcftoprs:
- modules/imputeme/vcftoprs/**
- tests/modules/imputeme/vcftoprs/**
Instrain profile (#1822) * add instrain profile * module instrain/profile * add instrain profile * module instrain/profile * instrain profile * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update * linting * Apply suggestions from code review * Update modules/instrain/profile/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-30 16:44:41 +00:00
instrain/profile:
- modules/instrain/profile/**
- tests/modules/instrain/profile/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
iqtree:
- modules/iqtree/**
- tests/modules/iqtree/**
Add a module for sra-tools prefetch (#714) * chore: apply module template * refactor: add NCBI settings to options * docs: complete meta information * feat: add prefetch process * fix: correct bash commands * tests: define the right tests * style: move option definition to satisfy linting * fix: extract version correctly * fix: correct newline issues * refactor: address review comments * Apply suggestions from code review * chore: add retrying via nf-core label * refactor: validate download thoroughly * refactor: remove vdb-config input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-11 21:30:41 +00:00
ismapper:
- modules/ismapper/**
- tests/modules/ismapper/**
New module: `isoseq3/cluster` (#801) * 📦 NEW: Add isoseq3/cluster module * 🐛FIX: Fix reports channel and add .pbi to it * 🐛FIX: Fix report channel definition * 👌IMPROVE: Move .pbi file into reports channel * 👌IMPROVE: remove --use_qvs option from command line * 👌 IMPROVE: Add in addParams removed options from command line * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: add singletons parameter and improve outputs * 🐛 FIX: Update test with last module model * 👌 IMPROVE: Add test tag * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update test data config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Remove unused index * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/cluster module * 🐛FIX: Fix reports channel and add .pbi to it * 🐛FIX: Fix report channel definition * 👌IMPROVE: Move .pbi file into reports channel * 👌IMPROVE: remove --use_qvs option from command line * 👌 IMPROVE: Add in addParams removed options from command line * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: add singletons parameter and improve outputs * 🐛 FIX: Update test with last module model * 👌 IMPROVE: Add test tag * 👌 IMPROVE: Update test data config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Remove unused index * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 📦 NEW: Add galgal6 chr30 test data * 📦 NEW: Add bamtools module * 👌 IMPROVE: Ignore test data * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update code to new versions capture + better output channels * 👌 IMPROVE: Update with new versions.yml file * 🐛 FIX: Update meta.yml + correct typos * 👌 IMPROVE: Clean output file names + correct typo * 🐛 FIX: Remove bamtools/split module from isoseq3/cluster
2021-10-07 09:06:02 +00:00
isoseq3/cluster:
- modules/isoseq3/cluster/**
- tests/modules/isoseq3/cluster/**
New module: `isoseq3/refine` (#748) * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Fill contains args * 👌 IMPROVE: Add one channel per output file * 👌 IMPROVE: Minor updates * 👌 IMPROVE: Minors Update - Remove TODO from test.yml - Remove useless piece of code * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Fill contains args * 📦 NEW: Add isoseq3/refine module * 👌 IMPROVE: Add parallelization * 🐛 FIX: Correct Typo * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The module accept one channel (primers moved into the first channel) * 👌 IMPROVE: Assign a value channel to primers input Improve workflow code readability * 👌 IMPROVE: Update to the version of templates * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Update test file * 👌 IMPROVE: Add one channel per output file * 👌 IMPROVE: Minor updates * 👌 IMPROVE: Minors Update - Remove TODO from test.yml - Remove useless piece of code * 🐛 FIX: Remove unwanted files * 🐛 FIX: Protect \ * 🐛 FIX: Remove test files * Apply suggestions from code review * Apply suggestions from code review * Update tests/modules/isoseq3/refine/test.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-06 10:13:48 +00:00
isoseq3/refine:
- modules/isoseq3/refine/**
- tests/modules/isoseq3/refine/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
ivar/consensus:
- modules/ivar/consensus/**
- tests/modules/ivar/consensus/**
ivar/trim:
- modules/ivar/trim/**
- tests/modules/ivar/trim/**
ivar/variants:
- modules/ivar/variants/**
- tests/modules/ivar/variants/**
Notebook modules (#617) * Draft rmarkdown module * stub jupyter notebook module * Create yaml file with params * Update meta.yml for rmarkdown module * Add comment on YAML * Update notebooks module, clean up parametrize.nf * Two separate channels for parameters and input files * Fix Rmd render script * Add tests for rmarkdown * Fix tests for rmarkdown module * Update checksums * Fix tests for jupyter * Test without Grab() * Update software versions * update rmarkdown dependencies * Draft for multiple versions * Fix indent of script * Fix indent in rmarkdown script * Emit version.syml * Update modules/rmarkdown/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/rmarkdown/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/rmarkdown/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Rename rmarkdown to rmarkdownnotebook * Add rmarkdown mulled biocontainer * Write sessionInfo to separate log file * Update rmarkdownnotebook * Sessioninfo does not have a stable md5sum * Update jupyternotebook * Update meta * Add jupyternotebook biocontainers * Handle Groovy Gstrings in parameterize * Update to versions.yml * Update functions.nf * Fix versions yaml * Fix EC lint * Update modules/rmarkdownnotebook/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/jupyternotebook/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Use official test data * Harshilify * Make parameters channel clearer * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Update main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-24 18:51:56 +00:00
jupyternotebook:
- modules/jupyternotebook/**
- tests/modules/jupyternotebook/**
Add kaiju_kaiju module (#1448) * Added kaiju_kaiju module * Update modules/kaiju/kaiju/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/kaiju/kaiju/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/kaiju/kaiju/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update keywords Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update output file naming * Update output file naming * update spacing for lint * Update input file patterns Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-03-28 12:28:50 +00:00
kaiju/kaiju:
- modules/kaiju/kaiju/**
- tests/modules/kaiju/kaiju/**
Add KAIJU2KRONA module (#1800) Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-23 16:38:50 +00:00
kaiju/kaiju2krona:
- modules/kaiju/kaiju2krona/**
- tests/modules/kaiju/kaiju2krona/**
Kaiju2table module (#1545) * Add kaiju2table module
2022-04-22 09:26:30 +00:00
kaiju/kaiju2table:
- modules/kaiju/kaiju2table/**
- tests/modules/kaiju/kaiju2table/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
kallisto/index:
- modules/kallisto/index/**
- tests/modules/kallisto/index/**
kallistobustools/count:
- modules/kallistobustools/count/**
- tests/modules/kallistobustools/count/**
kallistobustools/ref:
- modules/kallistobustools/ref/**
- tests/modules/kallistobustools/ref/**
Add module kat hist
2022-05-06 07:54:10 +00:00
kat/hist:
- modules/kat/hist/**
- tests/modules/kat/hist/**
Khmer normalizebymedian (#985) * Templates for new module * pe only test passing * only_pe and only_se passing * only_pe, only_se, mixed passes * Multiple pe + se tc passes * Passing args works * Add 'interleaved' to description * Fixed linting message * Update modules/khmer/normalizebymedian/main.nf Good point. Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2021-10-29 11:23:34 +00:00
khmer/normalizebymedian:
- modules/khmer/normalizebymedian/**
- tests/modules/khmer/normalizebymedian/**
Add khmer unique-kmers.py module (#1838)
2022-06-30 15:23:30 +00:00
khmer/uniquekmers:
- modules/khmer/uniquekmers/**
- tests/modules/khmer/uniquekmers/**
Add module `kleborate` (#711) * initial commit [ci skip] * remove todo from the module files [ci skip] * add a sample test case [ci skip] * push the latest work [ci skip] * bump kleborate build * test passing with the new build for kleborate [ci skip] * ready for review * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-21 19:45:42 +00:00
kleborate:
- modules/kleborate/**
- tests/modules/kleborate/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
kraken2/kraken2:
- modules/kraken2/kraken2/**
- modules/untar/**
- tests/modules/kraken2/kraken2/**
New module: krakentools/kreport2krona (#1746) * Add module definition for kreport2krona * Add metadata for kreport2krona module * Add tests for kreport2krona Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-06-13 18:14:44 +00:00
krakentools/kreport2krona:
- modules/krakentools/kreport2krona/**
- tests/modules/krakentools/kreport2krona/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
krona/kronadb:
- modules/krona/kronadb/**
- tests/modules/krona/kronadb/**
add Krona_db module (#995) * add Krona_db module * removed md5 sum * Update tests/modules/kronatools/kronadb/main.nf Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * added input information * removed trailing white spaces * changed krona version to 2.7.1 * Apply suggestions from code review * Update modules/kronatools/kronadb/meta.yml * Update modules/kronatools/kronadb/main.nf Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com>
2021-11-15 16:01:46 +00:00
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
krona/ktimporttaxonomy:
- modules/krona/ktimporttaxonomy/**
- tests/modules/krona/ktimporttaxonomy/**
add Kronatools KTImportTaxonomy (#928) * created and initialised krona module * Added kronatools/ktimporttaxonomy module * removing previous redundant work * added contains info for html * edited contains in test.yml * Update get versions Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * remove old syntax Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * rewording module description Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * added detailed keywords Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * update syntax and tool version * fixed meta.yml issues * remove contains line from test.yml * re-wrote module after nf-core/tools update - should work now * removed md5 * Update modules/kronatools/ktimporttaxonomy/main.nf Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * update meta save * removed typo * double quotes to single quotes around html * re-ran test, which updated md5 * removed md5 * 'classifier' removed to fix linting * update version * removed erroneous ktimporttaxonomy2 * Updated input to include meta and database * fixed tab issues in yaml * added `contains` to test.yml * edited `contains` in test.yml * trying another `contains` * retrying `contains` * contains with extra line * removed classifier from tag * Apply suggestions from code review * Update meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:40:46 +00:00
add kimporttext module (#1560) * add kimporttext module * fix the Prettier error. * fix the Prettier error. * fix the test.yml * fix the test.yml * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/krona/ktimporttext/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * update the test files; simplify the main script of krona/ktimporttext. * update the test file url for krona ktimporttext Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-28 12:16:26 +00:00
krona/ktimporttext:
- modules/krona/ktimporttext/**
- tests/modules/krona/ktimporttext/**
new module: md5sum
2022-05-06 07:20:40 +00:00
krona/ktupdatetaxonomy:
- modules/krona/ktupdatetaxonomy/**
- tests/modules/krona/ktupdatetaxonomy/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
last/dotplot:
- modules/last/dotplot/**
- tests/modules/last/dotplot/**
last/lastal:
- modules/last/lastal/**
- tests/modules/last/lastal/**
last/lastdb:
- modules/last/lastdb/**
- tests/modules/last/lastdb/**
last/mafconvert:
- modules/last/mafconvert/**
- tests/modules/last/mafconvert/**
last/mafswap:
- modules/last/mafswap/**
- tests/modules/last/mafswap/**
last/postmask:
- modules/last/postmask/**
- tests/modules/last/postmask/**
last/split:
- modules/last/split/**
- tests/modules/last/split/**
last/train:
- modules/last/train/**
- tests/modules/last/train/**
Add `leehom` module (#1052) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add leeHom module * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 14:26:06 +00:00
leehom:
- modules/leehom/**
- tests/modules/leehom/**
add module for legsta (#1319)
2022-02-19 00:42:18 +00:00
legsta:
- modules/legsta/**
- tests/modules/legsta/**
New module: `LIMA` (#719) * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 👌 IMPROVE: Add channel for each output * 👌 IMPROVE: Remove comments * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 🐛 FIX: Fill contains args * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 👌 IMPROVE: Add channel for each output * 👌 IMPROVE: Remove comments * 🐛 FIX: Clean test_data.config * Update modules/lima/main.nf Add meta to each output Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/lima/main.nf Remove useless parenthesis Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * 🐛 FIX: Keep version number only * 🐛 FIX: Reintegrate prefix variable and use it to define output file name * 👌 IMPROVE: add suffix arg to check output files names * 👌 IMPROVE: Use prefix for output filename * 🐛 FIX: Set optional output Allow usage of different input formats * 👌 IMPROVE: Update meta file * 👌 IMPROVE: Update test One test for each input file type * 👌 IMPROVE: add fasta, fastq.gz, fastq, fastq.gz test files * 👌 IMPROVE: Update with last templates / Follow new version.yaml rule * 🐛 FIX: Fix typos and include getProcessName function * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Using suffix to manage output was not a my best idea Add a bash code to detect extension and update output file name * 👌 IMPROVE: clean code Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2021-09-27 15:14:35 +00:00
lima:
- modules/lima/**
- tests/modules/lima/**
add lissero module (#1026) * add lissero module * Update test.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 19:52:07 +00:00
lissero:
- modules/lissero/**
- tests/modules/lissero/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
lofreq/call:
- modules/lofreq/call/**
- tests/modules/lofreq/call/**
lofreq/callparallel:
- modules/lofreq/callparallel/**
- tests/modules/lofreq/callparallel/**
lofreq/filter:
- modules/lofreq/filter/**
- tests/modules/lofreq/filter/**
lofreq/indelqual:
- modules/lofreq/indelqual/**
- tests/modules/lofreq/indelqual/**
Add new module macrel/contigs (#1109) * Add new module macrel/contigs * removed trailing whitespace * removed whitespace * linting cleanup * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Updated the test.yml It didnt upload the updated version earlier for some reason :( * Update test.yml * Update test.yml * Update test.yml as generated by pytest * Update test.yml * updated the version issue * Update tests/modules/macrel/contigs/test.yml * Update modules/macrel/contigs/main.nf * Update modules/macrel/contigs/main.nf * Update pytest_modules.yml * Update pytest_modules.yml * Update modules/macrel/contigs/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Zipped all fasta outputs * Update main.nf * Update test.yml * Update test.yml * Update main.nf * Update main.nf (gzip -n) * Update test.yml * Update main.nf * Update main.nf * Update test.yml * Update tests/modules/macrel/contigs/test.yml * Update modules/macrel/contigs/main.nf * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: darcy220606 <ananhamido@hotmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-12-09 12:17:50 +00:00
macrel/contigs:
- modules/macrel/contigs/**
- tests/modules/macrel/contigs/**
Macs2 calllpeak (#1038) * Add tests and yml file for macs2/callpeak * add format option for macs2 * update macs2/callpeak to accept format argument * update test.yml * update the container version. * try to fix the issue in conda container. * Update conda and containers * Going back to previous container versions Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-11-15 17:17:40 +00:00
macs2/callpeak:
- modules/macs2/callpeak/**
- tests/modules/macs2/callpeak/**
Add MAFFT module (#1351) Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-28 07:40:24 +00:00
mafft:
- modules/mafft/**
- tests/modules/mafft/**
module: MALT/BUILD (#645) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start MALT-build * Start MALT build (missing meta files and outputs specS) * Local tests * Correct test map_type * Finished module, just waiting for UNZIP module to finalise tests * Correct tests in preparation for Unzip * Ouptut log file too * Update meta.yml * Rename log file * Rename log file * Remove debugging stuff * Add Unzip module * Linting update * Linting update * Fix input db * Fix db file in cmd * Update modules/malt/build/main.nf * Update modules/malt/build/main.nf * Update main.nf
2021-08-03 14:24:19 +00:00
malt/build:
- modules/malt/build/**
- tests/modules/malt/build_test/**
module: MALT/RUN (#646) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add MALT with incomplete tests * Parameter typo fix * Clean up test yaml * Finish MALT module prior UNZIP and MALT_BUILD modiules * Add required modules for tests * Sync test out with malt-build * Fix input parameters in tests based on final build module * Update modules/malt/run/meta.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-08-04 09:06:08 +00:00
malt/run:
- modules/malt/run/**
- tests/modules/malt/run/**
add: MALTEXTRACT (#725) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start maltextract module * start tests * Get tests working now we have test data * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Changes after review * Update tests/modules/maltextract/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update tests/modules/maltextract/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update tests/modules/maltextract/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-09-21 18:57:27 +00:00
maltextract:
- modules/maltextract/**
- tests/modules/maltextract/**
add manta conversion script
2022-06-11 11:01:18 +00:00
manta/convertinversion:
- modules/manta/convertinversion/**
- tests/modules/manta/convertinversion/**
adding new manta/germline + manta/tumoronly modules (#906) * feat: all manta/single to modules * fix module name * fix module name * fix: changes from review comments * fix: test data
2021-10-27 16:24:48 +00:00
manta/germline:
- modules/manta/germline/**
- tests/modules/manta/germline/**
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912) * remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 14:14:52 +00:00
manta/somatic:
- modules/manta/somatic/**
- tests/modules/manta/somatic/**
adding new manta/germline + manta/tumoronly modules (#906) * feat: all manta/single to modules * fix module name * fix module name * fix: changes from review comments * fix: test data
2021-10-27 16:24:48 +00:00
manta/tumoronly:
- modules/manta/tumoronly/**
- tests/modules/manta/tumoronly/**
Add new module Mapdamage2 (#975) * Fitst attempt at mapdamage2 * Add new module mapdamage2 * Removed __pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc * Modify main.nf and meta.yml * Modify main.nf and meta.yml * Modify main.nf and meta.yml * Modify meta.yml * Update pytest_modules.yml * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * edit the meta.yml and main.nf after reviews * Update meta.yml * Update meta.yml Co-authored-by: AIbrahim <AIbrahim@apate.hki-jena.de> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-09 13:05:23 +00:00
mapdamage2:
- modules/mapdamage2/**
- tests/modules/mapdamage2/**
add module for mash dist (#1193) * add module for mash dist * fix lint Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2022-01-04 16:29:49 +00:00
mash/dist:
- modules/mash/dist/**
- tests/modules/mash/dist/**
Add mash screen
2022-05-20 13:23:11 +00:00
mash/screen:
- modules/mash/screen/**
- tests/modules/mash/screen/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
mash/sketch:
- modules/mash/sketch/**
- tests/modules/mash/sketch/**
add mashtree module (#767) * add mashtree module * remove todo * whitespace adjustment * remove un-reproducible md5sum * Update main.nf * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 20:27:30 +00:00
mashtree:
- modules/mashtree/**
- tests/modules/mashtree/**
New module: `maxbin2` (#895) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Added, just need to finish tests once we have bacterial data * Add prelim test data * Fix version reporting * Add tests based on proposed test-dataset * Finalise new testdata * Fix md5sum issue by removing it... * Update main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-26 21:07:33 +00:00
maxbin2:
- modules/maxbin2/**
- tests/modules/maxbin2/**
corrected entry
2022-01-19 14:45:52 +00:00
maxquant/lfq:
- modules/maxquant/lfq/**
added pytest
2022-01-03 10:33:17 +00:00
- tests/modules/maxquant/lfq/**
add module for mcroni (#1750) Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-06-13 13:04:01 +00:00
mcroni:
- modules/mcroni/**
- tests/modules/mcroni/**
new module: md5sum
2022-05-06 07:20:40 +00:00
md5sum:
- modules/md5sum/**
- tests/modules/md5sum/**
Add Medaka module (#992) * add racon * add medaka module * add medaka module * add medaka module * add medaka module * add medaka module * add medaka module * Indentation * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update main.nf * Update main.nf * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:26:37 +00:00
medaka:
- modules/medaka/**
- tests/modules/medaka/**
Add MEGAHIT (#810) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
2021-10-12 15:06:06 +00:00
megahit:
- modules/megahit/**
- tests/modules/megahit/**
Add MEGAN/DAA2INFO (#1848) * Add daa2info * Add right flag in the config * Fix config * Apply suggestions from code review Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-07-05 07:36:22 +00:00
megan/daa2info:
- modules/megan/daa2info/**
- tests/modules/megan/daa2info/**
Add MEGAN/RMA2INFO (#1513) * fix: remove left-over unnecessary code * Add megan/rma2info * Attempt at fixing test * Right yml formatting * Get the versios reporting correct
2022-04-12 06:35:36 +00:00
megan/rma2info:
- modules/megan/rma2info/**
- tests/modules/megan/rma2info/**
Add `leehom` module (#1052) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add leeHom module * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 14:26:06 +00:00
meningotype:
- modules/meningotype/**
- tests/modules/meningotype/**
Add Merqury (#1647) * Add merqury files * Remove md5sum for completeness stats file * update container and test output * Update modules/merqury/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Explicitly set thread usage for meryl * Remove empty file md5sum Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-07-14 08:38:50 +00:00
merqury:
- modules/merqury/**
- tests/modules/merqury/**
Add MerquryFK KatComp (#1797) Add Kat Comp Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-21 07:43:37 +00:00
merquryfk/katcomp:
- modules/merquryfk/katcomp/**
- tests/modules/merquryfk/katcomp/**
Add MerquryFK KatGC (#1798) * Add KAT GC * Add additional container warning
2022-06-23 18:57:15 +00:00
merquryfk/katgc:
- modules/merquryfk/katgc/**
- tests/modules/merquryfk/katgc/**
Add MerquryFK (#1778) * Add MerquryFK * Change resource allocation
2022-06-14 14:36:02 +00:00
merquryfk/merquryfk:
- modules/merquryfk/merquryfk/**
- tests/modules/merquryfk/merquryfk/**
Add MerquryFK PloidyPlot (#1780)
2022-06-14 18:50:58 +00:00
merquryfk/ploidyplot:
- modules/merquryfk/ploidyplot/**
- tests/modules/merquryfk/ploidyplot/**
Start Meryl count
2022-05-06 15:04:04 +00:00
meryl/count:
- modules/meryl/count/**
- tests/modules/meryl/count/**
Add meryl histogram
2022-05-09 08:50:28 +00:00
meryl/histogram:
- modules/meryl/histogram/**
- tests/modules/meryl/histogram/**
Add meryl unionsum
2022-05-09 08:33:21 +00:00
meryl/unionsum:
- modules/meryl/unionsum/**
- tests/modules/meryl/unionsum/**
New module: `metabat2` (#875) * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs/outpus * remove trailing whitespace * compressing and removing not reproducible md5sums * follow symlinks while decompressing * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * split tests * export env variable * Update modules/metabat2/jgisummarizebamcontigdepths/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * answer PR comments and switch to bgzip Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 20:08:26 +00:00
metabat2/jgisummarizebamcontigdepths:
- modules/metabat2/jgisummarizebamcontigdepths/**
- tests/modules/metabat2/jgisummarizebamcontigdepths/**
metabat2/metabat2:
- modules/metabat2/metabat2/**
- tests/modules/metabat2/metabat2/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
metaphlan3:
- modules/metaphlan3/**
- tests/modules/metaphlan3/**
methyldackel/extract:
- modules/methyldackel/extract/**
- tests/modules/methyldackel/extract/**
methyldackel/mbias:
- modules/methyldackel/mbias/**
- tests/modules/methyldackel/mbias/**
minia:
- modules/minia/**
- tests/modules/minia/**
Add Miniasm module (#962) * add racon * add miniasm module * edit miniasm module * edit miniasm module * Update tests/modules/racon/main.nf Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update tests/modules/racon/test.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update modules/miniasm/meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * Update main.nf Add some spaces. * Update meta.yml Correct DOI * Update main.nf * Apply suggestions from code review * Update tests/modules/miniasm/test.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:50:56 +00:00
miniasm:
- modules/miniasm/**
- tests/modules/miniasm/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
minimap2/align:
- modules/minimap2/align/**
- tests/modules/minimap2/align/**
minimap2/index:
- modules/minimap2/index/**
- tests/modules/minimap2/index/**
added classic mlst module (#742) * added classic mlst module * removed nf-core TODO comments * included drpatelh suggestions * adjust version capture identation * update main to pass lint * follow output expected by test.yml * suggested prefix change from rpetit3 * Apply suggestions from code review Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 19:49:46 +00:00
mlst:
- modules/mlst/**
- tests/modules/mlst/**
add mobsuite_recon module (#1270) * add mobsuite_recon module * Update main.nf * Update nextflow.config * Update test.yml Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-19 00:52:38 +00:00
mobsuite/recon:
- modules/mobsuite/recon/**
- tests/modules/mobsuite/recon/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
mosdepth:
- modules/mosdepth/**
- tests/modules/mosdepth/**
add module motus_downloaddb
2022-04-14 16:56:42 +00:00
motus/downloaddb:
- modules/motus/downloaddb/**
- tests/modules/motus/downloaddb/**
Add MOTUS/MERGE (#1734) * Add motus/merge module, missing test yml * Fix prefix * Fix polymersase * Update test meta.yml * Try new version system * Typo fix * Clairfy docs for the version file * Switch to directory auto detection * Now with the change and not just meta * Remove now unneeded input parameter from test * Fix input type check * Try adding db requirement to fix docker issue * Update modules/motus/merge/main.nf * Fix input * Apply suggestions from code review * Fix md5sums * Replace debugging db location with actual * Fix contains due to further varialbility * Indenting
2022-07-07 07:47:41 +00:00
motus/merge:
- modules/motus/merge/**
- tests/modules/motus/merge/**
init
2022-04-24 11:55:17 +00:00
motus/profile:
- modules/motus/profile/**
- tests/modules/motus/profile/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
msisensor/msi:
- modules/msisensor/msi/**
- tests/modules/msisensor/msi/**
msisensor/scan:
- modules/msisensor/scan/**
- tests/modules/msisensor/scan/**
Add msisensorpro (#1267) * Add msisensorpro * remove absolute paths * fixing tests * fix msisensorpro tests * Update modules/msisensorpro/msi_somatic/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update modules/msisensorpro/msi_somatic/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * add when back in * add when back in * Update modules/msisensorpro/msi_somatic/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * update description * Update main.nf * Update main.nf * Update main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-09 20:05:49 +00:00
msisensorpro/msi_somatic:
- modules/msisensorpro/msi_somatic/**
- tests/modules/msisensorpro/msi_somatic/**
msisensorpro/scan:
- modules/msisensorpro/scan/**
- tests/modules/msisensorpro/scan/**
Mtnucratio (#986) * add new module samtools_depth * fixed main.nf for samtools/depth * add new module mtnucratio * fix main.nf * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * layout in main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-29 13:02:02 +00:00
mtnucratio:
- modules/mtnucratio/**
- tests/modules/mtnucratio/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
multiqc:
- modules/fastqc/**
- modules/multiqc/**
- tests/modules/multiqc/**
Add MultiVCFAnalyzer (#1845) * Add MultiVCFAnalyzer * Fix versions * Fix tests due to md5sum var * Apply suggestions from code review * Linting * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-07-05 07:47:10 +00:00
multivcfanalyzer:
- modules/multivcfanalyzer/**
- tests/modules/multivcfanalyzer/**
Initial commit mummer module (#940)
2021-11-15 15:53:41 +00:00
mummer:
- modules/mummer/**
- tests/modules/mummer/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
muscle:
- modules/muscle/**
- tests/modules/muscle/**
nanolyse:
- modules/nanolyse/**
- tests/modules/nanolyse/**
nanoplot:
- modules/nanoplot/**
- tests/modules/nanoplot/**
add ncbi-genome-download module (#980) * add ncbi-genome-download module * Update modules/ncbigenomedownload/main.nf Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 18:32:53 +00:00
ncbigenomedownload:
- modules/ncbigenomedownload/**
- tests/modules/ncbigenomedownload/**
Add nextclade/datasetget and nextclade/run modules (#1210) * Remove old nextclade module * Add nextclade/datasetget and nextclade/run modules * Fix ECLint * Add reference and tag as inputs to datasetget module * Fix tests * Adjust spacing
2022-01-17 10:46:15 +00:00
nextclade/datasetget:
- modules/nextclade/datasetget/**
- tests/modules/nextclade/datasetget/**
nextclade/run:
- modules/nextclade/run/**
- tests/modules/nextclade/run/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
add ngmaster module (#1024) * add ngmaster module * add docker container Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-10 18:25:50 +00:00
ngmaster:
- modules/ngmaster/**
- tests/modules/ngmaster/**
New module: NGSCheckMate (#1290) NGSCheckMate ncm mode, working on bam files and vcf files to check that (human) samples match as expected Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-03-11 09:02:10 +00:00
ngscheckmate/ncm:
- modules/ngscheckmate/ncm/**
- tests/modules/ngscheckmate/ncm/**
add new nucmer module (#945) * add new nucmer module * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * update tests with file produced by input * Update main.nf * Update meta.yml Co-authored-by: Michael Cipriano <mcipriano@gmail.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 22:05:34 +00:00
nucmer:
- modules/nucmer/**
- tests/modules/nucmer/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
optitype:
- modules/optitype/**
- tests/modules/optitype/**
pairix:
- modules/pairix/**
- tests/modules/pairix/**
pairtools/dedup:
- modules/pairtools/dedup/**
- tests/modules/pairtools/dedup/**
pairtools/flip:
- modules/pairtools/flip/**
- tests/modules/pairtools/flip/**
pairtools/parse:
- modules/pairtools/parse/**
- tests/modules/pairtools/parse/**
pairtools/restrict:
- modules/pairtools/restrict/**
- tests/modules/pairtools/restrict/**
pairtools/select:
- modules/pairtools/select/**
- tests/modules/pairtools/select/**
pairtools/sort:
- modules/pairtools/sort/**
- tests/modules/pairtools/sort/**
add module for panaroo, fix pirate tests (#1444) * add module for panaroo * update pirate test yaml * update panaroo test yaml * update pirate test yaml md5s * Update main.nf * Update main.nf * pin bioperl version
2022-03-25 02:11:04 +00:00
panaroo/run:
- modules/panaroo/run/**
- tests/modules/panaroo/run/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
pangolin:
- modules/pangolin/**
- tests/modules/pangolin/**
add paraclu (#909) * add paraclu * remove TODOs * add min_cluster as input parameter, remove option parameters * add tool_dev_url
2021-10-27 13:48:49 +00:00
paraclu:
- modules/paraclu/**
- tests/modules/paraclu/**
New module: `pbbam/pbmerge` (#752) * 👌 IMPROVE: Add some pacbio test files * 📦 NEW: Add pbbam/pbmerge module * 🐛 FIX: Add optional arguments to command line * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update test data config and test script * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Add some pacbio test files * 📦 NEW: Add pbbam/pbmerge module * 🐛 FIX: Add optional arguments to command line * 👌 IMPROVE: Update to last templates version * 👌 IMPROVE: Update module to last template version * 👌 IMPROVE: Update test data config and test script * 👌 IMPROVE: Remove useless index + Fix Typos * 👌 IMPROVE: Update and clean code * 🐛 FIX: Update module path in test * 🐛 FIX: Add missing () + correct module path in test * 👌 IMPROVE: Update pbmerge from version 1.6.0 to 1.7.0 * 👌 IMPROVE: Change output filename suffix for something more generic * 🐛 Update test.yml * Apply suggestions from code review * Update tests/modules/pbbam/pbmerge/test.yml * Update tests/modules/pbbam/pbmerge/main.nf Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 22:16:45 +00:00
pbbam/pbmerge:
- modules/pbbam/pbmerge/**
- tests/modules/pbbam/pbmerge/**
new module: pbccs (#688) * 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 📦 NEW: First commit of pbccs module * 👌 IMPROVE: Remove option from command + rename output (ccs -> bam) * 👌 IMPROVE: Move .pbi output into report channel * 🐛FIX: Correct code after --rq option removal from command line module - module main.nf: Remove ramaining rq input channel - Test main.nf: Transfert rq into addParams - Test test.yml: Update md5sums * 🐛FIX: Repair additionnal option usage * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: CCS is run in parallel with --chunk option * 👌 IMPROVE: Add Pbindex in bam ouput channel * 👌 IMPROVE: Change label to process_low * 👌 IMPROVE: Define reports files names + add json version of txt report * 🐛 FIX: Add missing backslashes * 🐛 FIX: Add missing gz extension * 🐛 FIX: update ouput channel * 🐛 FIX: output file name * 👌 IMPROVE: .gitignore * 👌 IMPROVE: Update function.nf to last version * 👌 IMPROVE: Update saveAs in main.nf * 👌 IMPROVE: Add pbccs module * 🐛 FIX: Fix Broken test * 👌 IMPROVE: Update test_data.config * 🐛 FIX: Fix test * 👌 IMPROVE: Update path of test dataset files * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: fill contains args * 👌 IMPROVE: One output => One Channel * 👌 IMPROVE: One input => One channel * 🐛 FIX: Update tests * 🐛 FIX: Remove TODOs from test.yaml * 👌 IMPROVE: Revert and keep bam and pbi together * 🐛 FIX: Remove old rq input from meta.yml * 👌 IMPROVE: Update test to match input channels Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 10:48:18 +00:00
pbccs:
- modules/pbccs/**
- tests/modules/pbccs/**
add gatk4/gatherbqsr (#1130) * nf-core modules create * add module files * indent * remove templte code * manually revert pytest changes from tools * manually revert pytest changes from tools * add include statement back in Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-12-08 22:43:36 +00:00
peddy:
- modules/peddy/**
- tests/modules/peddy/**
Add task.ext.args to phantompeakqualtools and finish the module (#1474) * Add --max--ppsize option * Add args to phantompeakqualtools and all the missing files (test, yml, ...) * Fix tests * Add the nextflow.config * Fix tests
2022-03-31 21:59:21 +00:00
phantompeakqualtools:
- modules/phantompeakqualtools/**
- tests/modules/phantompeakqualtools/**
Add phyloflash module (#786) * initial stubs [ci skip] * remove comments and add main command [ci skip] * design iteration [ci skip] * add new standard functions.nf [ci skip] * update the version string [ci skip] * accomodate the db stubs and single/double ends [ci skip] * add FIXME for missing info [ci skip] * Accomodate the results folder [ci skip] * Update main.nf * Apply suggestions from code review * Update main.nf * Apply suggestions from code review * Add version file to stubs [ci skip] * Tweak the output dir pattern [ci skip] * Update modules/phyloflash/main.nf * Update modules/phyloflash/main.nf * Update modules/phyloflash/main.nf Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-21 19:43:58 +00:00
phyloflash:
- modules/phyloflash/**
- tests/modules/phyloflash/**
Picard addorreplacereadgroups (#1305) * add picard-addorreplacereadgroups * add picard_addorreplacereadgroups * add new line to main.nf * remove trailing whitespaces * remove trailing whitespaces * change to output in test yml * add when directive * picard 2.26.10 -> 2.26.9 * picard 2.26.10 -> 2.26.9 test yml Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-19 02:59:06 +00:00
picard/addorreplacereadgroups:
- modules/picard/addorreplacereadgroups/**
- tests/modules/picard/addorreplacereadgroups/**
Picard cleansam (#1306) * add picard-cleansam * add picard/cleansam * update test yml with output * picard 2.26.10 -> 2.26.9 * add output to test yml Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-19 02:17:58 +00:00
picard/cleansam:
- modules/picard/cleansam/**
- tests/modules/picard/cleansam/**
Picard/collecthsmetrics (#927) * added template * integrated module * added fasta index info * test works, have placeholder data for baits until test-data PR is merged * added new files to config * updated test files * fixing fails :sparkles: * okay final fix here on the md5sum :face_palm: * md5sum variable * update meta.yml to reflect consistency to main.nf * reverted version so conda works * Apply suggestions from code review Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * md5sum can't be generated consistently for output Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-10 09:52:54 +00:00
picard/collecthsmetrics:
- modules/picard/collecthsmetrics/**
- tests/modules/picard/collecthsmetrics/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
picard/collectmultiplemetrics:
- modules/picard/collectmultiplemetrics/**
- tests/modules/picard/collectmultiplemetrics/**
picard/collectwgsmetrics:
- modules/picard/collectwgsmetrics/**
- tests/modules/picard/collectwgsmetrics/**
Picard createsequencedictionary (#1310) * add picard/createsequencedictionary module * add picard-CreateSequenceDictionary * add picard/createsequencedictionary/ * add contains to test yml * update test yml contains * update test yml contains Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-19 01:49:12 +00:00
picard/createsequencedictionary:
- modules/picard/createsequencedictionary/**
- tests/modules/picard/createsequencedictionary/**
Tool/crosscheckfingerprints (#1505) * first commit * first commit * update test.yml * update test.yml * Update modules/picard/crosscheckfingerprints/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update modules/picard/crosscheckfingerprints/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * add support for vcf haplotype maps * update test * update test data config, use test data * fix exit code * Update modules/picard/crosscheckfingerprints/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/crosscheckfingerprints/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * remove unused stub Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-08 14:02:10 +00:00
picard/crosscheckfingerprints:
- modules/picard/crosscheckfingerprints/**
- tests/modules/picard/crosscheckfingerprints/**
module: picard filtersamreads (#602) * Start work filtersamreads * Refactored to allow optional input * Use proper readlist test data * Remove typo * Fix if else condition * Remove debugging code * Fix container URLs * Add required input specification meta * Cleanup * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Fix suffixing * Additional formatting tweaks * Update modules/picard/filtersamreads/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/picard/filtersamreads/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 14:22:19 +00:00
picard/filtersamreads:
- modules/picard/filtersamreads/**
- tests/modules/picard/filtersamreads/**
Picard fixmateinformation (#1315) * add picard-fixmateinformation * add picard-fixmateinformation * fix trailing whitespace * fix trailing whitespace Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-02-19 01:18:05 +00:00
picard/fixmateinformation:
- modules/picard/fixmateinformation/**
- tests/modules/picard/fixmateinformation/**
Picard liftover vcf (#1431) * Building Picard liftovervcf module * Building Picard liftovervcf module_test * Building Picard liftovervcf pytest * Module for picard liftover vcf created * Fixed files after linting test * Fixed trailing whitespace * Checked files with prettier * further formatting with prettier * Fixed test.yml * Fixed input variable names * Changed contain test.liftef.vcf * Changed contain in test.yml test.liftef.vcf * Run prittier * Going back to previous version of test.yml * downgrading picard to 2.26.10 from 2.26.11 * Update modules/picard/liftovervcf/main.nf Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/main.nf Print available memory Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Output from .vcf to .vcf.gz * Added spaces to align emit * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/picard/liftovervcf/meta.yml Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> * Removing md5sum test Co-authored-by: jemten <jemten@users.noreply.github.com> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-04-07 11:50:58 +00:00
picard/liftovervcf:
- modules/picard/liftovervcf/**
- tests/modules/picard/liftovervcf/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
picard/markduplicates:
- modules/picard/markduplicates/**
- tests/modules/picard/markduplicates/**
picard/mergesamfiles:
- modules/picard/mergesamfiles/**
- tests/modules/picard/mergesamfiles/**
module: picard sortsam (#603) * Add picard/sortsam module * Fix container links * Changes after code review * Input meta in the right place
2021-07-21 11:48:07 +00:00
picard/sortsam:
- modules/picard/sortsam/**
- tests/modules/picard/sortsam/**
Add picard/sortvcf (#1370) * sortvcf * add files * update meta * update java mem * update documentation link * remove todo * review suggestions * fix test.yml * fix conda error * fix version code
2022-03-03 16:40:16 +00:00
picard/sortvcf:
- modules/picard/sortvcf/**
- tests/modules/picard/sortvcf/**
add pirate module (#777) * new module pirate * remove md5 check for non reproducible binary files * get those to-dos out * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:28:25 +00:00
pirate:
- modules/pirate/**
- tests/modules/pirate/**
add module for plasmidfinder (#1773) * add module for plasmidfinder * Update test.yml
2022-06-15 16:25:51 +00:00
plasmidfinder:
- modules/plasmidfinder/**
- tests/modules/plasmidfinder/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
plasmidid:
- modules/plasmidid/**
- tests/modules/plasmidid/**
Implement `plink/extract` module (#901) * Implement PLINK_EXTRACT module * fix plink version number * Update main.nf * Update test_data.config * Update modules/plink/extract/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * just use one channel * fix test with new channel input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-09 14:03:13 +00:00
plink/extract:
- modules/plink/extract/**
- tests/modules/plink/extract/**
Adding plink/vcf module (#656) * adding plink module using nf-core tool [ci skip] * Restructures the project for plink/vcf (#1) * Add version string for plink * Create a plink/vcf module * small tweaks on main.nf and started to test [ci skip] * small changes on test args, local test with docker passed! * Update plink/vcf module listing * Update tag * fix tags as per linting guidelines * revert to the original state of tags * adding --threads to `main.nf` and `meta.yml` information Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com>
2021-09-14 06:51:40 +00:00
plink/vcf:
- modules/plink/vcf/**
- tests/modules/plink/vcf/**
New module: `plink2/extract` (#1228) * add plink2_extract * fix test yml path * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * compress output * add DOI * make outputs less ambiguous * update test for compressed output * brain is dumb * Update modules/plink2/extract/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-02-03 10:42:56 +00:00
plink2/extract:
- modules/plink2/extract/**
- tests/modules/plink2/extract/**
implement plink2/score module (#1259) * implement plink2/score module * fix test yml * fix typo :( * set cpu * set mem * fix input process input block * fix tests Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-03-07 18:02:40 +00:00
plink2/score:
- modules/plink2/score/**
- tests/modules/plink2/score/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
plink2/vcf:
- modules/plink2/vcf/**
- tests/modules/plink2/vcf/**
add new module pmdtools/filter #847 (#963) * commit but won't be used because pmdtools should have a submodule * added submodule pmdtools/filter * removed pmdtools module created before deciding to design two submodules * oops forgot to remove a TODO * removed white space meta.yml, removed v in version and manually added submodule /filter to test * Update pytest_modules.yml * Update main.nf added split_cpus for multi-tools module resources * Update test.yml added .pmd extension to match modules/ main.nf * Update test.yml update md5sum * Update singularity and docker build in main.nf From build 4 to 5 in order to match the conda one * Update modules/pmdtools/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf adding samtools version we need both pmdtools and samtools versions * Update main.nf remove .pmd extension * Update test.yml md5sum Because file extension changed Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-13 15:09:14 +00:00
pmdtools/filter:
- modules/pmdtools/filter/**
- tests/modules/pmdtools/filter/**
add `porechop` module (#914) * add module main porechop * update porechop main * add porechop functions * update meta porechop * add test main porechop * add porechop pytest yml * add porechop test.yml * Update modules/porechop/meta.yml Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * re-add porechop avoid conflict * Update modules/porechop/meta.yml Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * fix prefix suffix Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2021-10-28 11:21:36 +00:00
porechop:
- modules/porechop/**
- tests/modules/porechop/**
Split preseq lcextrap and ccurve (#1440) * fix(preseq): Update lcextrap file name * chore(preseq): Bump lcextrap image * feat: Initialize preseq c_curve * docs(preseq): Update documentation
2022-03-25 17:11:40 +00:00
preseq/ccurve:
- modules/preseq/ccurve/**
- tests/modules/preseq/ccurve/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
preseq/lcextrap:
- modules/preseq/lcextrap/**
- tests/modules/preseq/lcextrap/**
Add PRINSEQPLUSPLUS (#1481) * fix: remove left-over unnecessary code * Add prinseq++ * Remove last todo * Fix tests due to variability of output FASTQs (reads can be ordered differently between runs) * Apply suggestions from code review
2022-04-03 14:06:22 +00:00
prinseqplusplus:
- modules/prinseqplusplus/**
- tests/modules/prinseqplusplus/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
prodigal:
- modules/prodigal/**
- tests/modules/prodigal/**
prokka:
- modules/prokka/**
- tests/modules/prokka/**
pycoqc:
- modules/pycoqc/**
- tests/modules/pycoqc/**
Add pydamage analyze module (#705) * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * simplify PR to analyze subcommand Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 12:03:51 +00:00
pydamage/analyze:
- modules/pydamage/analyze/**
- tests/modules/pydamage/analyze/**
Add PyDamage filter (#713) * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-09-16 13:05:49 +00:00
pydamage/filter:
- modules/pydamage/filter/**
- tests/modules/pydamage/filter/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
qcat:
- modules/qcat/**
- tests/modules/qcat/**
qualimap/bamqc:
- modules/qualimap/bamqc/**
- tests/modules/qualimap/bamqc/**
add qualimap with cram files + remove val from qualimap/bam, instead use empty list as everywhere else (#1320) Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-18 08:43:53 +00:00
qualimap/bamqccram:
- modules/qualimap/bamqccram/**
- tests/modules/qualimap/bamqccram/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
quast:
- modules/quast/**
- tests/modules/quast/**
Add Racon module to nf-core/modules (#949) * add racon * add racon * add racon * add racon module * add racon module * edit racon module * edit racon module * edit racon module * edit racon module Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2021-10-29 12:33:38 +00:00
racon:
- modules/racon/**
- tests/modules/racon/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
rapidnj:
- modules/rapidnj/**
- tests/modules/rapidnj/**
rasusa:
- modules/rasusa/**
- tests/modules/rasusa/**
Raven assembler (#1087) Adding a new module for [Raven](https://github.com/lbcb-sci/raven), a De novo genome assembler for long uncorrected reads.
2022-02-01 10:47:01 +00:00
raven:
- modules/raven/**
- tests/modules/raven/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
raxmlng:
- modules/raxmlng/**
- tests/modules/raxmlng/**
add module for rgi (#1321) * add module for rgi * fix extension * fix test yaml * Update main.nf * Update main.nf
2022-02-19 00:23:44 +00:00
rgi/main:
- modules/rgi/main/**
- tests/modules/rgi/main/**
template
2022-06-07 10:14:40 +00:00
rhocall/annotate:
- modules/rhocall/annotate/**
- tests/modules/rhocall/annotate/**
Notebook modules (#617) * Draft rmarkdown module * stub jupyter notebook module * Create yaml file with params * Update meta.yml for rmarkdown module * Add comment on YAML * Update notebooks module, clean up parametrize.nf * Two separate channels for parameters and input files * Fix Rmd render script * Add tests for rmarkdown * Fix tests for rmarkdown module * Update checksums * Fix tests for jupyter * Test without Grab() * Update software versions * update rmarkdown dependencies * Draft for multiple versions * Fix indent of script * Fix indent in rmarkdown script * Emit version.syml * Update modules/rmarkdown/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/rmarkdown/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/rmarkdown/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Rename rmarkdown to rmarkdownnotebook * Add rmarkdown mulled biocontainer * Write sessionInfo to separate log file * Update rmarkdownnotebook * Sessioninfo does not have a stable md5sum * Update jupyternotebook * Update meta * Add jupyternotebook biocontainers * Handle Groovy Gstrings in parameterize * Update to versions.yml * Update functions.nf * Fix versions yaml * Fix EC lint * Update modules/rmarkdownnotebook/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/jupyternotebook/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Use official test data * Harshilify * Make parameters channel clearer * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Update main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-24 18:51:56 +00:00
rmarkdownnotebook:
- modules/rmarkdownnotebook/**
- tests/modules/rmarkdownnotebook/**
add roary module (#776) * add module roary * Update meta.yml * Update meta.yml * Update meta.yml * Update meta.yml * Update main.nf * Update meta.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:08:47 +00:00
roary:
- modules/roary/**
- tests/modules/roary/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
rsem/calculateexpression:
- modules/rsem/calculateexpression/**
- tests/modules/rsem/calculateexpression/**
rsem/preparereference:
- modules/rsem/preparereference/**
- tests/modules/rsem/preparereference/**
rseqc/bamstat:
- modules/rseqc/bamstat/**
- tests/modules/rseqc/bamstat/**
rseqc/inferexperiment:
- modules/rseqc/inferexperiment/**
- tests/modules/rseqc/inferexperiment/**
rseqc/innerdistance:
- modules/rseqc/innerdistance/**
- tests/modules/rseqc/innerdistance/**
rseqc/junctionannotation:
- modules/rseqc/junctionannotation/**
- tests/modules/rseqc/junctionannotation/**
rseqc/junctionsaturation:
- modules/rseqc/junctionsaturation/**
- tests/modules/rseqc/junctionsaturation/**
rseqc/readdistribution:
- modules/rseqc/readdistribution/**
- tests/modules/rseqc/readdistribution/**
rseqc/readduplication:
- modules/rseqc/readduplication/**
- tests/modules/rseqc/readduplication/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
rseqc/tin:
- modules/rseqc/tin/**
- tests/modules/rseqc/tin/**
new module rtgtools/pedfilter (#1777) * new module rtgtools/pedfilter * removed checksum due to the presence of a date in the file
2022-06-14 14:02:18 +00:00
rtgtools/pedfilter:
- modules/rtgtools/pedfilter/**
- tests/modules/rtgtools/pedfilter/**
Added the version.yml
2022-05-04 14:51:09 +00:00
rtgtools/vcfeval:
- modules/rtgtools/vcfeval/**
- tests/modules/rtgtools/vcfeval/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
salmon/index:
- modules/salmon/index/**
- tests/modules/salmon/index/**
salmon/quant:
- modules/salmon/quant/**
- tests/modules/salmon/quant/**
New module: Samblaster (#954) * add base code from samblaster * added test yml * fixing versions files, should this be the cause of online lint failures * removed tmp files that shouldn't be there * fixing output file name - 1 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fixing output file name - 2 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fixing output file name - 3 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fixing output file name - 4 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fixing output file name - 5 Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fixing output file name - 6 * fixed indent * fixed input name and updated test.yml file with new name Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-04 17:18:56 +00:00
samblaster:
- modules/samblaster/**
- tests/modules/samblaster/**
Add samtools ampliconclip (#590) * created template for `samtools/ampliconclip` (#584) * All tests passing (#584) * Linting fixed (#584) * Final linting fixed (#584) * Optional output flags moved to `input` (#584) * typo fix (#584) * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-20 20:31:31 +00:00
samtools/ampliconclip:
- modules/samtools/ampliconclip/**
- tests/modules/samtools/ampliconclip/**
Bam2fq (#958) * added template for module * update main * added specific code * wrong variable name in else script * added tests for both split and nosplit * docker test successful - updating yaml * adding echo to version print
2021-10-29 08:46:34 +00:00
samtools/bam2fq:
- modules/samtools/bam2fq/**
- tests/modules/samtools/bam2fq/**
Add samtools/collatefastq module (#1536) * add samtools/collatefastq module * update yml file * improve output
2022-04-20 08:05:17 +00:00
samtools/collatefastq:
- modules/samtools/collatefastq/**
- tests/modules/samtools/collatefastq/**
added gatk4/splitintervals
2022-05-13 11:46:34 +00:00
samtools/convert:
- modules/samtools/convert/**
- tests/modules/samtools/convert/**
add new module samtools/depth (#950) * add new module samtools_depth * fixed main.nf for samtools/depth * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-28 10:53:21 +00:00
samtools/depth:
- modules/samtools/depth/**
- tests/modules/samtools/depth/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
samtools/faidx:
- modules/samtools/faidx/**
- tests/modules/samtools/faidx/**
samtools/fastq:
- modules/samtools/fastq/**
- tests/modules/samtools/fastq/**
Samtools fixmate module (#991) * Samtools fixmate module * Update modules/samtools/fixmate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf * Update modules/samtools/fixmate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update meta.yml Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-01 12:12:14 +00:00
samtools/fixmate:
- modules/samtools/fixmate/**
- tests/modules/samtools/fixmate/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
samtools/flagstat:
- modules/samtools/flagstat/**
- tests/modules/samtools/flagstat/**
samtools/idxstats:
- modules/samtools/idxstats/**
- tests/modules/samtools/idxstats/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
samtools/index:
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
- modules/samtools/index/**
- tests/modules/samtools/index/**
samtools/merge:
- modules/samtools/merge/**
- tests/modules/samtools/merge/**
samtools/mpileup:
- modules/samtools/mpileup/**
- tests/modules/samtools/mpileup/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
samtools/sort:
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
- modules/samtools/sort/**
- tests/modules/samtools/sort/**
samtools/stats:
- modules/samtools/stats/**
- tests/modules/samtools/stats/**
samtools/view:
- modules/samtools/view/**
- tests/modules/samtools/view/**
add scoary module (#1034) Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-06 15:34:39 +00:00
scoary:
- modules/scoary/**
- tests/modules/scoary/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
seacr/callpeak:
- modules/seacr/callpeak/**
- tests/modules/seacr/callpeak/**
Seqkit pair (#1348) * add seqkit pair module * local tests * local tests * fix workflow name * fix workflow name * fix version indentation * fix version indentation * fix version indentation * fix review comments * fix review comments * fix github usernames * minor fix * add meta unpaired output Co-authored-by: Peri <rrx8@cdc.gov>
2022-02-24 14:07:35 +00:00
seqkit/pair:
- modules/seqkit/pair/**
- tests/modules/seqkit/pair/**
added module seqkit replace (#1382) * added module seqkit replace * added when * removed extra line * Update modules/seqkit/replace/main.nf Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * Updated meta * updated indents Co-authored-by: Cipriano <rrn8@cdc.gov> Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-03-09 17:36:05 +00:00
seqkit/replace:
- modules/seqkit/replace/**
- tests/modules/seqkit/replace/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
seqkit/split2:
- modules/seqkit/split2/**
- tests/modules/seqkit/split2/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
feat: add module for seqkit stats (#1466)
2022-03-30 21:01:17 +00:00
seqkit/stats:
- modules/seqkit/stats/**
- tests/modules/seqkit/stats/**
add seqsero2 module (#1016) * add seqsero2 module * correct lint errors * Update modules/seqsero2/main.nf Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> * set output directory Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
2021-11-04 07:49:30 +00:00
seqsero2:
- modules/seqsero2/**
- tests/modules/seqsero2/**
add new assembly scan module (#971) * add new assembly scan module * add newline endings * fix newline ending * add newline at end Co-authored-by: Peri <rrx8@cdc.gov> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-10-29 08:01:23 +00:00
seqtk/mergepe:
- modules/seqtk/mergepe/**
- tests/modules/seqtk/mergepe/**
Seqtk rename (#1304) * Added seqtk/rename module and tests code * Updated files and testing code for seqtk rename * Added meta map to seqtk/rename module def * updated prefix parameter usage * updated test.yml to remove local filepaths --> change to output * Added empty line to main.nf
2022-02-16 16:28:08 +00:00
seqtk/rename:
- modules/seqtk/rename/**
- tests/modules/seqtk/rename/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
seqtk/sample:
- modules/seqtk/sample/**
- tests/modules/seqtk/sample/**
Seqtk seq (#1340) * Initial commit of seqtk/seq module files * pytest.yml * updated module and tests code, need to finish modules/main.nf * Initial commit of seqtk/seq module files * pytest.yml * updated module and tests code, need to finish modules/main.nf * Adding code and configs for seqtk/seq module * Re-tested module following minor code update * removed trailing whitespace errors * Changed variable name to following reviewer suggestions Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-23 16:02:51 +00:00
seqtk/seq:
- modules/seqtk/seq/**
- tests/modules/seqtk/seq/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
seqtk/subseq:
- modules/seqtk/subseq/**
- tests/modules/seqtk/subseq/**
sequenzautils/bam2seqz:
- modules/sequenzautils/bam2seqz/**
- tests/modules/sequenzautils/bam2seqz/**
sequenzautils/gcwiggle:
- modules/sequenzautils/gcwiggle/**
- tests/modules/sequenzautils/gcwiggle/**
seqwish/induce:
- modules/seqwish/induce/**
- tests/modules/seqwish/induce/**
Add Sexdeterrmine module
2022-04-29 12:28:45 +00:00
sexdeterrmine:
- modules/sexdeterrmine/**
- tests/modules/sexdeterrmine/**
added sha256sum
2022-05-06 08:28:14 +00:00
shasum:
- modules/shasum/**
- tests/modules/shasum/**
add module for shigatyper
2022-04-21 18:49:42 +00:00
shigatyper:
- modules/shigatyper/**
- tests/modules/shigatyper/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
shovill:
- modules/shovill/**
- tests/modules/shovill/**
module: snp-dists (#697) * initial commit for draft [ci skip] * baseline code [ci skip] * update the test [ci skip] * finalize the description and all tests passing * accomodate optional args [ci skip] * fix the leftover todo statement * Update modules/snpdists/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 15:36:49 +00:00
add module for sistr (#1323) * add module for sistr * Update test.yml
2022-02-19 00:33:48 +00:00
sistr:
- modules/sistr/**
- tests/modules/sistr/**
feat: add module for slimfastq
2022-05-02 21:16:59 +00:00
slimfastq:
- modules/slimfastq/**
- tests/modules/slimfastq/**
fix linting
2022-05-06 12:16:38 +00:00
snapaligner/align:
- modules/snapaligner/align/**
- tests/modules/snapaligner/align/**
Tool/snap aligner single (#1510) * first commit * add tool * fix tests * fix indents * Update modules/snapaligner/single/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix comments * fix versions * prettier Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-12 09:20:35 +00:00
Add meryl histogram
2022-05-09 08:50:28 +00:00
snapaligner/index:
- modules/snapaligner/index/**
- tests/modules/snapaligner/index/**
add module for snippy
2022-05-10 21:31:43 +00:00
snippy/run:
- modules/snippy/run/**
- tests/modules/snippy/run/**
module: snp-dists (#697) * initial commit for draft [ci skip] * baseline code [ci skip] * update the test [ci skip] * finalize the description and all tests passing * accomodate optional args [ci skip] * fix the leftover todo statement * Update modules/snpdists/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 15:36:49 +00:00
snpdists:
- modules/snpdists/**
- tests/modules/snpdists/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
snpeff:
- modules/snpeff/**
- tests/modules/snpeff/**
Added new module snpsift/split (#1031) * added new module snpsift/split * added options.args * added .vcf.gz to input * removed test and updated to new NF DSL2 syntax * Updated to new NF DSL2 syntax * added option to join vcf files Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-12-17 08:08:14 +00:00
snpsift/split:
- modules/snpsift/split/**
- tests/modules/snpsift/split/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
snpsites:
- modules/snpsites/**
- tests/modules/snpsites/**
feat: add sourmash sketch (#1287) Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:30:28 +00:00
sourmash/sketch:
- modules/sourmash/sketch/**
- tests/modules/sourmash/sketch/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
spades:
- modules/spades/**
- tests/modules/spades/**
add spatyper module (#784) * add spatyper module * lint fix * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-05 21:21:35 +00:00
spatyper:
- modules/spatyper/**
- tests/modules/spatyper/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
sratools/fasterqdump:
Add a new module for fasterq-dump (#807) * chore: use template to create fasterq module * feat: add fasterq-dump process module * docs: provide input and output descriptions * docs: add comment on `--temp` * fix: use correct variable * tests: define test output * refactor: address review comments * refactor: remove vdb-config input * chore: add new test data to config * tests: define single-end and paired-end cases * refactor: choose specific output * tests: do not expect single FASTQ for paired-end * feat: add compression * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * tests: revert the test data name * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-10-12 13:20:58 +00:00
- modules/sratools/fasterqdump/**
- tests/modules/sratools/fasterqdump/**
Add RSeqC tin.py module (#1174) * Add RSeqC tin.py module * Fix EC lint for unrelated hmmcopy module * Remove md5sum for empty file
2021-12-15 21:26:43 +00:00
sratools/prefetch:
Add strelka/somatic module (#866) * Add strelka/somatic module * Fill out meta.yml properly
2021-10-18 21:34:23 +00:00
- modules/sratools/prefetch/**
- tests/modules/sratools/prefetch/**
adding srst2 module
2022-04-27 22:01:28 +00:00
srst2/srst2:
- modules/srst2/srst2/**
- tests/modules/srst2/srst2/**
add module for ssuisero (#1329) * add module for ssuisero * Update main.nf * Update meta.yml Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
2022-02-28 03:04:03 +00:00
ssuissero:
- modules/ssuissero/**
- tests/modules/ssuissero/**
new tool: staden_io_lib (#1499) * new tool: staden_io_lib * update docker containers * add test.yml * add fai index input * typo * fix version.yml * update md5sum * omit md5sum for cram * move scramble to submodule * add missing in/output * remove some comments Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-08 13:54:15 +00:00
stadeniolib/scramble:
- modules/stadeniolib/scramble/**
- tests/modules/stadeniolib/scramble/**
add staphopia-sccmec module (#702) * add staphopia-sccmec module * add additional test * change output name * Update main.nf * Update test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-15 16:24:11 +00:00
staphopiasccmec:
- modules/staphopiasccmec/**
- tests/modules/staphopiasccmec/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
star/align:
- modules/star/align/**
- tests/modules/star/align/**
star/genomegenerate:
- modules/star/genomegenerate/**
- tests/modules/star/genomegenerate/**
Add stranger (#1360) * Add stranger * Add when clause * Update paths * Update modules/stranger/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-03-01 13:29:46 +00:00
stranger:
- modules/stranger/**
- tests/modules/stranger/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
strelka/germline:
- modules/strelka/germline/**
- tests/modules/strelka/germline/**
Add strelka/somatic module (#866) * Add strelka/somatic module * Fill out meta.yml properly
2021-10-18 21:34:23 +00:00
strelka/somatic:
- modules/strelka/somatic/**
- tests/modules/strelka/somatic/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
stringtie/merge:
- modules/stringtie/merge/**
- tests/modules/stringtie/merge/**
stringtie/stringtie:
- modules/stringtie/stringtie/**
- tests/modules/stringtie/stringtie/**
subread/featurecounts:
- modules/subread/featurecounts/**
- tests/modules/subread/featurecounts/**
Add svdb/merge (#1233) * nf-core create * svdb merge module and test * remove to-do from test.yml * version * update meta.yml * add stub * add when
2022-02-04 14:29:44 +00:00
svdb/merge:
- modules/svdb/merge/**
- tests/modules/svdb/merge/**
Add svdb/query (#1249) * first commit * add test data
2022-02-01 19:46:10 +00:00
svdb/query:
- modules/svdb/query/**
- tests/modules/svdb/query/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
tabix/bgzip:
- modules/tabix/bgzip/**
- tests/modules/tabix/bgzip/**
tabix/bgziptabix:
- modules/tabix/bgziptabix/**
- tests/modules/tabix/bgziptabix/**
tabix/tabix:
- modules/tabix/tabix/**
- tests/modules/tabix/tabix/**
add module for tbprofiler (#947) * add module for tbprofiler * Update test.yml * Update meta.yml Co-authored-by: Abhinav Sharma <abhi18av@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 14:35:55 +00:00
tbprofiler/profile:
- modules/tbprofiler/profile/**
- tests/modules/tbprofiler/profile/**
Transdecoder predict (#1251) * create transdecoder/longorf module * module transdecoder * main.nf * transdecoder/longorf ready to PR * review comments update * transdecoder/predict module create * test transdecoder/predict module * fix pytest * pytest passed * removed whitespace * Update meta.yml * Update meta.yml Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2022-02-02 08:46:07 +00:00
test/template:
- modules/test/template/**
- tests/modules/test/template/**
Add TIDDIT cov (#822) * added template for tiddit/cov * test finished * quick fix to meta info * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * applying suggestions Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-10-13 10:59:35 +00:00
tiddit/cov:
- modules/tiddit/cov/**
- tests/modules/tiddit/cov/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
tiddit/sv:
- modules/tiddit/sv/**
- tests/modules/tiddit/sv/**
Transdecoder longorf (#1230) * create transdecoder/longorf module * module transdecoder * main.nf * transdecoder/longorf ready to PR * review comments update * transdecoder_longorf reviewed main.nf * removed predict * test.yml updated * pytest run Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se>
2022-01-31 12:34:38 +00:00
transdecoder/longorf:
- modules/transdecoder/longorf/**
- tests/modules/transdecoder/longorf/**
Transdecoder predict (#1251) * create transdecoder/longorf module * module transdecoder * main.nf * transdecoder/longorf ready to PR * review comments update * transdecoder/predict module create * test transdecoder/predict module * fix pytest * pytest passed * removed whitespace * Update meta.yml * Update meta.yml Co-authored-by: Danilo Di Leo <danilo.dileo@lnu.se> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2022-02-02 08:46:07 +00:00
transdecoder/predict:
- modules/transdecoder/predict/**
- tests/modules/transdecoder/predict/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
trimgalore:
- modules/trimgalore/**
- tests/modules/trimgalore/**
Trimmomatic (#1757) * Trimmomatic main only first draft * Add test files * SE PE Adjustment * Remove extra reads input * chore: Remove TODOs * Apply suggestions from code review Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * fix(trimmomatic): Handle SE output correctly Since there's never going to be unpaired reads for SE reads we can get away with it for SE * fix(trimmomatic): Use correct elvis operator to handle logic * fix(trimmomatic): Add hack to work with SE and PE reads * Update test.yml * use the PE and SE trimming correctly * Made user set adaptors * Add documentation * test(trimmomatic): Add files to pytest_modules * test(trimmomatic): Update name of failing test Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-06-17 13:18:15 +00:00
trimmomatic:
- modules/trimmomatic/**
- tests/modules/trimmomatic/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
ucsc/bed12tobigbed:
- modules/ucsc/bed12tobigbed/**
- tests/modules/ucsc/bed12tobigbed/**
ucsc/bedclip:
- modules/ucsc/bedclip/**
- tests/modules/ucsc/bedclip/**
ucsc/bedgraphtobigwig:
- modules/ucsc/bedgraphtobigwig/**
- tests/modules/ucsc/bedgraphtobigwig/**
ucsc/bigwigaverageoverbed:
- modules/ucsc/bigwigaverageoverbed/**
- tests/modules/ucsc/bigwigaverageoverbed/**
New module: ucsc/liftover (#868) * add liftOver module * add liftover module tests * fix getProcessName * fix tests * fix out of date function * version numbers should be numeric * drop versions.yml from test.yml * Update modules/ucsc/liftover/main.nf Remove software name variable Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update tests/modules/ucsc/liftover/main.nf Use test chain file Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * add genome_chain_gz to test data config * update md5sum for new chain test data * Fix indentation in file declaration Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-10-21 16:04:15 +00:00
ucsc/liftover:
- modules/ucsc/liftover/**
- tests/modules/ucsc/liftover/**
New module: `checkm/lineagewf` (#899) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Added but test failing due to null on output channel * fix prefix variable * Complete checkm_lineagewf * Remove TODOs * Add description of fasta_ext parameter * Improve meta map for this context * Update meta.yml * Update modules/checkm/lineagewf/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
2021-10-26 20:54:10 +00:00
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
ucsc/wigtobigwig:
- modules/ucsc/wigtobigwig/**
- tests/modules/ucsc/wigtobigwig/**
New modules: `ultra/index` and `ultra/align` (#1830) * Add ultra/index and ultra/align modules * Correct tag and prefix * Fix typos * Remove SAMTOOLS SORT from test * Update: Convert sam to bam * Add tag to docker image * Fix typo * Add args2 for samtools
2022-07-04 06:46:49 +00:00
ultra/align:
- modules/ultra/align/**
- tests/modules/ultra/align/**
ultra/index:
- modules/ultra/index/**
- tests/modules/ultra/index/**
New module: `Ultra` (#871) * 👌 IMPROVE: Update .gitignore * 📦 Add ultra module * 👌 IMPROVE: Update test input * 👌 IMPROVE: Update and clean code - Update to last versions.yml file - Update meta.yml - Correct typos * 👌 IMPROVE: Update output channels + Rename following subtool * 👌 IMPROVE: Remove old ultre files * 👌 IMPROVE: Update of pytest_modules.yml * 👌 IMPROVE: Update test.yml * 👌 IMPROVE: Keep md5sum as much as possible * 👌 IMPROVE: Remove old ultra files * 👌 IMPROVE: Update of pytest_modules.yml * 👌 IMPROVE: Update test.yml * 👌 IMPROVE: Keep md5sum as much as possible * 🐛 Fix: add unsaved modifications * 🐛 FIX: Remove one inconstant md5sum * 🐛 FIX: Grab software name using ${getSoftwareName(task.process)} * 🐛 FIX: Remove md5sums for pickle files (not constant). * Update modules/ultra/pipeline/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/ultra/pipeline/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * 👌 IMPROVE: update output directory, update meta.yml * 👌 IMPROVE: Use modules to gunzip and sort gtf * 🐛 FIX: Set up channel correctly * 👌 IMPROVE: Remove pickles files and databases Those data might be useful in a debugging purpose. * Apply suggestions from code review * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 15:57:58 +00:00
ultra/pipeline:
- modules/ultra/pipeline/**
- tests/modules/ultra/pipeline/**
Add tests for umitools extract and dedup (#1429) * NGSCheckMate v1 * Add some tests for UMItools * Added tests for dedup * Include pytest * Delete main.nf * Delete meta.yml * Delete main.nf * Delete nextflow.config * Delete test.yml * add prettier * Add direct test on bam * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/modules/umitools/dedup/main.nf Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Update tests/config/pytest_modules.yml Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com> * Not ignore-umi Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-03-25 14:25:07 +00:00
umitools/dedup:
- modules/umitools/dedup/**
- modules/umitools/extract/**
- tests/modules/umitools/dedup/**
umitools/extract:
- modules/umitools/extract/**
- tests/modules/umitools/extract/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
unicycler:
- modules/unicycler/**
- tests/modules/unicycler/**
untar:
- modules/untar/**
- tests/modules/untar/**
module: unzip (#642) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add unzip module * Remove missing TODOs update mtea * Apply changes after code-review from @grst * Account for user trying to supply two input archives * Remove debugging test * Update modules/unzip/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Correct output path Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-08-02 07:40:57 +00:00
unzip:
- modules/unzip/**
- tests/modules/unzip/**
created the module
2022-04-27 09:12:58 +00:00
vardictjava:
- modules/vardictjava/**
- tests/modules/vardictjava/**
Add variantbam (#618) * template created for variantbam (#616) * Add bcftools reheader (#585) (#608) * local tests and linting passing (#585) * fix: picard filtersamreads input (#610) * Move readlist into same input channel as bam * Update test reflecting input restructuring * Update tests/modules/picard/filtersamreads/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix test Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added module arriba (#611) * Updated the version of STAR in align and genomegenerate modules * Changes in test.yml * Changes in test.yml * Added module arriba * Changes in test configs * Added module Arriba for fusion detection * Fixed review comments * Added an output option for discarded fusions * Resolved some conflits * conflicts * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * added test for new header * enhance module fastp: add `save_merged` (#598) (#614) * enhance module fastp: add `save_merged` (#598) * removed md5sum checks from log and json * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com> * fixed autogenerated biocontainter links * variantbam module passing all tests/lints (#616) * Added an optional output junction channel in STAR (#621) * Added an optional output channel for chimeric junctions * Fix in test.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * removed qcreport output fixes #616 Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: praveenraj2018 <43108054+praveenraj2018@users.noreply.github.com>
2021-07-26 18:07:29 +00:00
variantbam:
- modules/variantbam/**
- tests/modules/variantbam/**
new module vcf2db (#1795) * added vcf2db * fix test.yml * possible fix for failing tests * fix version number * fix test.yml * removed some comments
2022-06-17 13:54:02 +00:00
vcf2db:
- modules/vcf2db/**
- tests/modules/vcf2db/**
vcf2maf module with built in VEP (#1768) vcf2maf module created Additions: - vcf2maf module created - If VEP is present in PATH, it is added to command - If VEP is missing, it is ignored (recommended to skip with --inhibit-vep) - VEP version automatically added to versions.yml - Uses VEP cache during testing which is added to test-datasets in https://github.com/nf-core/test-datasets/pull/563 - Default Docker image includes VEP and vcf2maf - Test includes without VEP. Relates to #490
2022-06-20 16:27:12 +00:00
vcf2maf:
- modules/vcf2maf/**
- tests/modules/vcf2maf/**
New module/vcfanno (#1204) * boilerplate * tests passed * fixed regex Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>
2022-01-20 08:46:31 +00:00
vcfanno:
- modules/vcfanno/**
- tests/modules/vcfanno/**
Add new vcflib/vcfuniq module (#1208) * Add new vcflib/vcfuniq module * Rename module from vcfutils to vcfuniq * Fix tests * Compress output by default * Fix ECLint
2022-01-14 18:18:11 +00:00
vcflib/vcfuniq:
- modules/vcflib/vcfuniq/**
- tests/modules/vcflib/vcfuniq/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
vcftools:
- modules/vcftools/**
- tests/modules/vcftools/**
Add vserach usearch_global
2022-05-23 08:01:55 +00:00
vsearch/usearchglobal:
- modules/vsearch/usearchglobal/**
- tests/modules/vsearch/usearchglobal/**
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
yara/index:
- modules/yara/index/**
- tests/modules/yara/index/**
yara/mapper:
- modules/yara/mapper/**
- tests/modules/yara/mapper/**
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