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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/**
adapterremoval:
- modules/adapterremoval/**
- tests/modules/adapterremoval/**
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/**
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/**
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/**
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 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/**
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/**
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/**
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/**
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/**
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/**
bedtools/subtract:
- modules/bedtools/subtract/**
- tests/modules/bedtools/subtract/**
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/**
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/**
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
cellranger/mkref:
- modules/cellranger/mkref/**
- tests/modules/cellranger/mkref/**
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/**
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
cnvkit:
- modules/cnvkit/**
- tests/modules/cnvkit/**
cooler/digest:
- modules/cooler/digest/**
- tests/modules/cooler/digest/**
cooler/dump:
- modules/cooler/dump/**
- tests/modules/cooler/dump/**
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/**
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/**
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 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/**
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/**
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/**
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/**
ensemblvep:
- modules/ensemblvep/**
- tests/modules/ensemblvep/**
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/**
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/**
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/**
fasttree:
- modules/fasttree/**
- tests/modules/fasttree/**
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/**
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/**
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
freebayes:
- modules/freebayes/**
- tests/modules/freebayes/**
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/**
gatk4/baserecalibrator:
- modules/gatk4/baserecalibrator/**
- tests/modules/gatk4/baserecalibrator/**
gatk4/bedtointervallist:
- modules/gatk4/bedtointervallist/**
- tests/modules/gatk4/bedtointervallist/**
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
gatk4/calculatecontamination:
- modules/gatk4/calculatecontamination/**
- tests/modules/gatk4/calculatecontamination/**
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/**
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
gatk4/createsomaticpanelofnormals:
- 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/**
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
gatk4/filtermutectcalls:
- modules/gatk4/filtermutectcalls/**
- tests/modules/gatk4/filtermutectcalls/**
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
gatk4/getpileupsummaries:
- 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/**
gatk4/intervallisttools:
- modules/gatk4/intervallisttools/**
- tests/modules/gatk4/intervallisttools/**
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
gatk4/learnreadorientationmodel:
- modules/gatk4/learnreadorientationmodel/**
- tests/modules/gatk4/learnreadorientationmodel/**
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/**
gatk4/mergebamalignment:
- modules/gatk4/mergebamalignment/**
- tests/modules/gatk4/mergebamalignment/**
gatk4/mergevcfs:
- modules/gatk4/mergevcfs/**
- tests/modules/gatk4/mergevcfs/**
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
gatk4/mutect2:
- modules/gatk4/mutect2/**
- tests/modules/gatk4/mutect2/**
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/splitncigarreads:
- modules/gatk4/splitncigarreads/**
- tests/modules/gatk4/splitncigarreads/**
gatk4/variantfiltration:
- modules/gatk4/variantfiltration/**
- tests/modules/gatk4/variantfiltration/**
genmap/index:
- modules/genmap/index/**
- tests/modules/genmap/index/**
genmap/mappability:
- modules/genmap/mappability/**
- tests/modules/genmap/mappability/**
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/**
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/**
gunzip:
- modules/gunzip/**
- tests/modules/gunzip/**
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/**
hmmer/hmmalign:
- modules/hmmer/hmmalign/**
- tests/modules/hmmer/hmmalign/**
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/**
- tests/modules/homer/findpeaks/**
homer/maketagdirectory:
- modules/homer/maketagdirectory/**
- tests/modules/homer/maketagdirectory/**
homer/makeucscfile:
- modules/homer/makeucscfile/**
- tests/modules/homer/makeucscfile/**
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/**
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 `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/**
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/**
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/**
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/**
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/**
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/**
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/**
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/**
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/**
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/**
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/**
msisensor/msi:
- modules/msisensor/msi/**
- tests/modules/msisensor/msi/**
msisensor/scan:
- modules/msisensor/scan/**
- tests/modules/msisensor/scan/**
multiqc:
- modules/fastqc/**
- modules/multiqc/**
- tests/modules/multiqc/**
muscle:
- modules/muscle/**
- tests/modules/muscle/**
nanolyse:
- modules/nanolyse/**
- tests/modules/nanolyse/**
nanoplot:
- modules/nanoplot/**
- tests/modules/nanoplot/**
nextclade:
- modules/nextclade/**
- tests/modules/nextclade/**
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/**
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/**
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/**
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/**
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 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/**
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/**
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/**
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/**
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/**
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/**
quast:
- modules/quast/**
- tests/modules/quast/**
rapidnj:
- modules/rapidnj/**
- tests/modules/rapidnj/**
rasusa:
- modules/rasusa/**
- tests/modules/rasusa/**
raxmlng:
- modules/raxmlng/**
- tests/modules/raxmlng/**
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/**
salmon/index:
- modules/salmon/index/**
- tests/modules/salmon/index/**
salmon/quant:
- modules/salmon/quant/**
- tests/modules/salmon/quant/**
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 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/flagstat:
- modules/samtools/flagstat/**
- tests/modules/samtools/flagstat/**
samtools/idxstats:
- modules/samtools/idxstats/**
- tests/modules/samtools/idxstats/**
samtools/index:
- 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/**
samtools/sort:
- 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/**
seacr/callpeak:
- modules/seacr/callpeak/**
- tests/modules/seacr/callpeak/**
seqkit/split2:
- modules/seqkit/split2/**
- tests/modules/seqkit/split2/**
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/**
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/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/**
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
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/**
snpsites:
- modules/snpsites/**
- tests/modules/snpsites/**
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 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
sratools/fasterqdump:
- modules/sratools/fasterqdump/**
- tests/modules/sratools/fasterqdump/**
Add strelka/somatic module (#866) * Add strelka/somatic module * Fill out meta.yml properly
2021-10-18 21:34:23 +00:00
sratools/prefetch:
- modules/sratools/prefetch/**
- tests/modules/sratools/prefetch/**
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/**
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/**
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 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/**
trimgalore:
- modules/trimgalore/**
- tests/modules/trimgalore/**
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/**
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/**
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/**
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/**
yara/index:
- modules/yara/index/**
- tests/modules/yara/index/**
yara/mapper:
- modules/yara/mapper/**
- tests/modules/yara/mapper/**
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