nf-core_modules/tests/config/pytest_modules.yml

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abacas:
- modules/abacas/**
- tests/modules/abacas/**
adapterremoval:
- modules/adapterremoval/**
- tests/modules/adapterremoval/**
agrvate:
- modules/agrvate/**
- tests/modules/agrvate/**
allelecounter:
- modules/allelecounter/**
- tests/modules/allelecounter/**
amps:
- modules/amps/**
- tests/modules/amps/**
arriba:
- modules/arriba/**
- tests/modules/arriba/**
artic/guppyplex:
- modules/artic/guppyplex/**
- tests/modules/artic/guppyplex/**
artic/minion:
- modules/artic/minion/**
- tests/modules/artic/minion/**
assemblyscan:
- modules/assemblyscan/**
- tests/modules/assemblyscan/**
ataqv/ataqv:
- modules/ataqv/ataqv/**
- tests/modules/ataqv/ataqv/**
bakta:
- modules/bakta/**
- tests/modules/bakta/**
bamaligncleaner:
- modules/bamaligncleaner/**
- tests/modules/bamaligncleaner/**
2021-10-12 12:43:08 +00:00
bamtools/split:
- modules/bamtools/split/**
- tests/modules/bamtools/split/**
bamutil/trimbam:
- modules/bamutil/trimbam/**
- tests/modules/bamutil/trimbam/**
bandage/image:
- modules/bandage/image/**
- tests/modules/bandage/image/**
2021-09-20 09:27:34 +00:00
bbmap/align:
- modules/bbmap/align/**
- tests/modules/bbmap/align/**
bbmap/bbduk:
- modules/bbmap/bbduk/**
- tests/modules/bbmap/bbduk/**
bbmap/bbsplit:
- modules/bbmap/bbsplit/**
- tests/modules/bbmap/bbsplit/**
2021-09-03 07:28:28 +00:00
bbmap/index:
- modules/bbmap/index/**
- tests/modules/bbmap/index/**
bcftools/concat:
- modules/bcftools/concat/**
- tests/modules/bcftools/concat/**
bcftools/consensus:
- modules/bcftools/consensus/**
- tests/modules/bcftools/consensus/**
bcftools/filter:
- modules/bcftools/filter/**
- tests/modules/bcftools/filter/**
bcftools/index:
- modules/bcftools/index/**
- tests/modules/bcftools/index**
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/**
bcftools/norm:
- modules/bcftools/norm/**
- tests/modules/bcftools/norm/**
bcftools/query:
- modules/bcftools/query/**
- tests/modules/bcftools/query/**
bcftools/reheader:
- modules/bcftools/reheader/**
- tests/modules/bcftools/reheader/**
bcftools/sort:
- modules/bcftools/sort/**
- tests/modules/bcftools/sort/**
bcftools/stats:
- modules/bcftools/stats/**
- tests/modules/bcftools/stats/**
bcftools/view:
- modules/bcftools/view/**
- tests/modules/bcftools/view/**
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/**
bedtools/makewindows:
- modules/bedtools/makewindows/**
- tests/modules/bedtools/makewindows/**
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/**
bwa/aln:
- modules/bwa/aln/**
- tests/modules/bwa/aln/**
bwa/index:
- modules/bwa/index/**
- tests/modules/bwa/index/**
bwa/mem:
- modules/bwa/mem/**
- tests/modules/bwa/mem/**
bwa/sampe:
- modules/bwa/sampe/**
- tests/modules/bwa/sampe/**
bwa/samse:
- modules/bwa/samse/**
- tests/modules/bwa/samse/**
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:
- modules/cat/cat/**
- tests/modules/cat/cat/**
cat/fastq:
- modules/cat/fastq/**
- tests/modules/cat/fastq/**
cellranger/count:
- modules/cellranger/count/**
- tests/modules/cellranger/count/**
- modules/cellranger/mkref/**
- tests/modules/cellranger/mkref/**
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
cellranger/gtf:
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
cellranger/mkfastq:
- modules/cellranger/mkfastq/**
- tests/modules/cellranger/mkfastq/**
cellranger/mkgtf:
- modules/cellranger/mkgtf/**
- tests/modules/cellranger/mkgtf/**
cellranger/mkref:
- modules/cellranger/mkref/**
- tests/modules/cellranger/mkref/**
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
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/**
clonalframeml:
- modules/clonalframeml/**
- tests/modules/clonalframeml/**
Add new module: cmseq/polymut (#918) * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs/outpus * remove trailing whitespace * first cmseq commit * compressing and removing not reproducible md5sums * save intermediate work * follow symlinks while decompressing * add cmseq/polymut * add polymut * add extra test with optional input file * remove metabat2 * Update modules/cmseq/polymut/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix file extension * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add test without bam index * split tests in workflows * answer PR review * report version from variable Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-09 15:12:51 +00:00
cmseq/polymut:
- modules/cmseq/polymut/**
- tests/modules/cmseq/polymut/**
cnvkit/batch:
- modules/cnvkit/batch/**
- tests/modules/cnvkit/batch/**
cooler/cload:
- modules/cooler/cload/**
- tests/modules/cooler/cload/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
cooler/digest:
- modules/cooler/digest/**
- tests/modules/cooler/digest/**
cooler/dump:
- modules/cooler/dump/**
- tests/modules/cooler/dump/**
cooler/merge:
- modules/cooler/merge/**
- tests/modules/cooler/merge/**
cooler/zoomify:
- modules/cooler/zoomify/**
- tests/software/cooler/zoomify/**
csvtk/concat:
- modules/csvtk/concat/**
- tests/modules/csvtk/concat/**
csvtk/split:
- modules/csvtk/split/**
- tests/modules/csvtk/split/**
custom/dumpsoftwareversions:
- modules/custom/dumpsoftwareversions/**
- tests/modules/custom/dumpsoftwareversions/**
custom/getchromsizes:
- modules/custom/getchromsizes/**
- tests/modules/custom/getchromsizes/**
cutadapt:
- modules/cutadapt/**
- tests/modules/cutadapt/**
damageprofiler:
- modules/damageprofiler/**
- tests/modules/damageprofiler/**
Add new module: Das Tool (#1004) * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs/outpus * remove trailing whitespace * compressing and removing not reproducible md5sums * follow symlinks while decompressing * add dastool/scaffolds2bin * add dastool * remove non reproducible md5sum check for compressed files * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * split tests * export env variable * remove metabat2 from PR * fix linting errors * remove traling whitespace * Update modules/metabat2/jgisummarizebamcontigdepths/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * answer PR comments and switch to bgzip * PR review updates * update from PR review * update test files * add bacillus fragilis alignments * switch tests to bacillus fragilis * add string check * update test string * add pr comment answer * last fixes for PR review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-19 07:33:29 +00:00
dastool/dastool:
- modules/dastool/dastool/**
- tests/modules/dastool/dastool/**
dastool/scaffolds2bin:
- modules/dastool/scaffolds2bin/**
- tests/modules/dastool/scaffolds2bin/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
dedup:
- modules/dedup/**
- tests/modules/dedup/**
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/**
deepvariant:
- modules/deepvariant/**
- tests/modules/deepvariant/**
delly/call:
- modules/delly/call/**
- tests/modules/delly/call/**
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/**
diamond/blastx:
- modules/diamond/blastx/**
- tests/modules/diamond/blastx/**
Diamond (#710) * Added diamond * minor tweaks & yml fix * Fixed spacing issues due to failing lint * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-09-23 08:13:04 +00:00
diamond/makedb:
- modules/diamond/makedb/**
- tests/modules/diamond/makedb/**
dragmap/align:
- modules/dragmap/align/**
- tests/modules/dragmap/align/**
dragmap/hashtable:
- modules/dragmap/hashtable/**
- tests/modules/dragmap/hashtable/**
dragonflye:
- modules/dragonflye/**
- tests/modules/dragonflye/**
dshbio/exportsegments:
- modules/dshbio/exportsegments/**
- tests/modules/dshbio/exportsegments/**
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/**
ectyper:
- modules/ectyper/**
- tests/modules/ectyper/**
emmtyper:
- modules/emmtyper/**
- tests/modules/emmtyper/**
ensemblvep:
- modules/ensemblvep/**
- tests/modules/ensemblvep/**
expansionhunter:
- modules/expansionhunter/**
- tests/modules/expansionhunter/**
fargene:
- modules/fargene/**
- tests/modules/fargene/**
fastani:
- modules/fastani/**
- tests/modules/fastani/**
fastp:
- modules/fastp/**
- tests/modules/fastp/**
fastqc:
- modules/fastqc/**
- tests/modules/fastqc/**
fastqscan:
- modules/fastqscan/**
- tests/modules/fastqscan/**
fasttree:
- modules/fasttree/**
- tests/modules/fasttree/**
fgbio/callmolecularconsensusreads:
- modules/fgbio/callmolecularconsensusreads/**
- tests/modules/fgbio/callmolecularconsensusreads/**
fgbio/fastqtobam:
- modules/fgbio/fastqtobam/**
- tests/modules/fgbio/fastqtobam/**
fgbio/groupreadsbyumi:
- modules/fgbio/groupreadsbyumi/**
- tests/modules/fgbio/groupreadsbyumi/**
fgbio/sortbam:
- modules/fgbio/sortbam/**
- tests/modules/fgbio/sortbam/**
2021-10-27 15:00:11 +00:00
filtlong:
- modules/filtlong/**
- tests/modules/filtlong/**
flash:
- modules/flash/**
- tests/modules/flash/**
freebayes:
- modules/freebayes/**
- tests/modules/freebayes/**
gatk4/applybqsr:
- modules/gatk4/applybqsr/**
- tests/modules/gatk4/applybqsr/**
gatk4/applyvqsr:
- modules/gatk4/applyvqsr/**
- tests/modules/gatk4/applyvqsr/**
gatk4/baserecalibrator:
- modules/gatk4/baserecalibrator/**
- tests/modules/gatk4/baserecalibrator/**
gatk4/bedtointervallist:
- modules/gatk4/bedtointervallist/**
- tests/modules/gatk4/bedtointervallist/**
gatk4/calculatecontamination:
- modules/gatk4/calculatecontamination/**
- tests/modules/gatk4/calculatecontamination/**
gatk4/createsequencedictionary:
- modules/gatk4/createsequencedictionary/**
- tests/modules/gatk4/createsequencedictionary/**
gatk4/createsomaticpanelofnormals:
- modules/gatk4/createsomaticpanelofnormals/**
- tests/modules/gatk4/createsomaticpanelofnormals/**
gatk4/estimatelibrarycomplexity:
- modules/gatk4/estimatelibrarycomplexity/**
- tests/modules/gatk4/estimatelibrarycomplexity/**
gatk4/fastqtosam:
- modules/gatk4/fastqtosam/**
- tests/modules/gatk4/fastqtosam/**
gatk4/filtermutectcalls:
- modules/gatk4/filtermutectcalls/**
- tests/modules/gatk4/filtermutectcalls/**
gatk4/gatherbqsrreports:
- modules/gatk4/gatherbqsrreports/**
- tests/modules/gatk4/gatherbqsrreports/**
gatk4/genomicsdbimport:
- modules/gatk4/genomicsdbimport/**
- tests/modules/gatk4/genomicsdbimport/**
gatk4/genotypegvcfs:
- modules/gatk4/genotypegvcfs/**
- tests/modules/gatk4/genotypegvcfs/**
gatk4/getpileupsummaries:
- modules/gatk4/getpileupsummaries/**
- tests/modules/gatk4/getpileupsummaries/**
gatk4/haplotypecaller:
- modules/gatk4/haplotypecaller/**
- tests/modules/gatk4/haplotypecaller/**
gatk4/indexfeaturefile:
- modules/gatk4/indexfeaturefile/**
- tests/modules/gatk4/indexfeaturefile/**
gatk4/intervallisttools:
- modules/gatk4/intervallisttools/**
- tests/modules/gatk4/intervallisttools/**
gatk4/learnreadorientationmodel:
- modules/gatk4/learnreadorientationmodel/**
- tests/modules/gatk4/learnreadorientationmodel/**
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/**
gatk4/mutect2:
- modules/gatk4/mutect2/**
- tests/modules/gatk4/mutect2/**
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/**
gatk4/variantrecalibrator:
- modules/gatk4/variantrecalibrator/**
- tests/modules/gatk4/variantrecalibrator/**
genmap/index:
- modules/genmap/index/**
- tests/modules/genmap/index/**
genmap/mappability:
- modules/genmap/mappability/**
- tests/modules/genmap/mappability/**
genrich:
- modules/genrich/**
- tests/modules/genrich/**
gffread:
- modules/gffread/**
- tests/modules/gffread/**
glnexus:
- modules/glnexus/**
- tests/modules/glnexus/**
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/**
gtdbtk/classifywf:
- modules/gtdbtk/classifywf/**
- tests/modules/gtdbtk/classifywf/**
gubbins:
- modules/gubbins/**
- tests/modules/gubbins/**
gunc/downloaddb:
- modules/gunc/downloaddb/**
- tests/modules/gunc/downloaddb/**
gunc/run:
- modules/gunc/run/**
- tests/modules/gunc/run/**
gunzip:
- modules/gunzip/**
- tests/modules/gunzip/**
hicap:
- modules/hicap/**
- tests/modules/hicap/**
hifiasm:
- modules/hifiasm/**
- tests/modules/hifiasm/**
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/**
hmmcopy/gccounter:
- modules/hmmcopy/gccounter/**
- tests/modules/hmmcopy/gccounter/**
hmmcopy/generatemap:
- modules/hmmcopy/generatemap/**
- tests/modules/hmmcopy/generatemap/**
hmmcopy/mapcounter:
- modules/hmmcopy/mapcounter/**
- tests/modules/hmmcopy/mapcounter/**
hmmcopy/readcounter:
- modules/hmmcopy/readcounter/**
- tests/modules/hmmcopy/readcounter/**
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/**
idr:
- modules/idr/**
- tests/modules/idr/**
Add `leehom` module (#1052) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add leeHom module * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 14:26:06 +00:00
imputeme/vcftoprs:
- modules/imputeme/vcftoprs/**
- tests/modules/imputeme/vcftoprs/**
iqtree:
- modules/iqtree/**
- tests/modules/iqtree/**
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/**
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/**
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/**
khmer/normalizebymedian:
- modules/khmer/normalizebymedian/**
- tests/modules/khmer/normalizebymedian/**
kleborate:
- modules/kleborate/**
- tests/modules/kleborate/**
kraken2/kraken2:
- modules/kraken2/kraken2/**
- modules/untar/**
- tests/modules/kraken2/kraken2/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
krona/kronadb:
- modules/krona/kronadb/**
- tests/modules/krona/kronadb/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
krona/ktimporttaxonomy:
- modules/krona/ktimporttaxonomy/**
- tests/modules/krona/ktimporttaxonomy/**
add Kronatools KTImportTaxonomy (#928) * created and initialised krona module * Added kronatools/ktimporttaxonomy module * removing previous redundant work * added contains info for html * edited contains in test.yml * Update get versions Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * remove old syntax Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * rewording module description Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * added detailed keywords Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * update syntax and tool version * fixed meta.yml issues * remove contains line from test.yml * re-wrote module after nf-core/tools update - should work now * removed md5 * Update modules/kronatools/ktimporttaxonomy/main.nf Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> * update meta save * removed typo * double quotes to single quotes around html * re-ran test, which updated md5 * removed md5 * 'classifier' removed to fix linting * update version * removed erroneous ktimporttaxonomy2 * Updated input to include meta and database * fixed tab issues in yaml * added `contains` to test.yml * edited `contains` in test.yml * trying another `contains` * retrying `contains` * contains with extra line * removed classifier from tag * Apply suggestions from code review * Update meta.yml Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com> Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-11-15 17:40:46 +00:00
last/dotplot:
- modules/last/dotplot/**
- tests/modules/last/dotplot/**
last/lastal:
- modules/last/lastal/**
- tests/modules/last/lastal/**
last/lastdb:
- modules/last/lastdb/**
- tests/modules/last/lastdb/**
last/mafconvert:
- modules/last/mafconvert/**
- tests/modules/last/mafconvert/**
last/mafswap:
- modules/last/mafswap/**
- tests/modules/last/mafswap/**
last/postmask:
- modules/last/postmask/**
- tests/modules/last/postmask/**
last/split:
- modules/last/split/**
- tests/modules/last/split/**
last/train:
- modules/last/train/**
- tests/modules/last/train/**
Add `leehom` module (#1052) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add leeHom module * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 14:26:06 +00:00
leehom:
- modules/leehom/**
- tests/modules/leehom/**
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/**
lissero:
- modules/lissero/**
- tests/modules/lissero/**
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/**
macrel/contigs:
- modules/macrel/contigs/**
- tests/modules/macrel/contigs/**
macs2/callpeak:
- modules/macs2/callpeak/**
- tests/modules/macs2/callpeak/**
malt/build:
- modules/malt/build/**
- tests/modules/malt/build_test/**
malt/run:
- modules/malt/run/**
- tests/modules/malt/run/**
maltextract:
- modules/maltextract/**
- tests/modules/maltextract/**
manta/germline:
- modules/manta/germline/**
- tests/modules/manta/germline/**
manta/somatic:
- modules/manta/somatic/**
- tests/modules/manta/somatic/**
manta/tumoronly:
- modules/manta/tumoronly/**
- tests/modules/manta/tumoronly/**
mapdamage2:
- modules/mapdamage2/**
- tests/modules/mapdamage2/**
mash/dist:
- modules/mash/dist/**
- tests/modules/mash/dist/**
mash/sketch:
- modules/mash/sketch/**
- tests/modules/mash/sketch/**
mashtree:
- modules/mashtree/**
- tests/modules/mashtree/**
maxbin2:
- modules/maxbin2/**
- tests/modules/maxbin2/**
medaka:
- modules/medaka/**
- tests/modules/medaka/**
megahit:
- modules/megahit/**
- tests/modules/megahit/**
Add `leehom` module (#1052) * Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Add leeHom module * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/leehom/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2021-11-15 14:26:06 +00:00
meningotype:
- modules/meningotype/**
- tests/modules/meningotype/**
New module: `metabat2` (#875) * add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs/outpus * remove trailing whitespace * compressing and removing not reproducible md5sums * follow symlinks while decompressing * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * split tests * export env variable * Update modules/metabat2/jgisummarizebamcontigdepths/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * answer PR comments and switch to bgzip Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-11-08 20:08:26 +00:00
metabat2/jgisummarizebamcontigdepths:
- modules/metabat2/jgisummarizebamcontigdepths/**
- tests/modules/metabat2/jgisummarizebamcontigdepths/**
metabat2/metabat2:
- modules/metabat2/metabat2/**
- tests/modules/metabat2/metabat2/**
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/**
miniasm:
- modules/miniasm/**
- tests/modules/miniasm/**
minimap2/align:
- modules/minimap2/align/**
- tests/modules/minimap2/align/**
minimap2/index:
- modules/minimap2/index/**
- tests/modules/minimap2/index/**
mlst:
- modules/mlst/**
- tests/modules/mlst/**
mosdepth:
- modules/mosdepth/**
- tests/modules/mosdepth/**
msisensor/msi:
- modules/msisensor/msi/**
- tests/modules/msisensor/msi/**
msisensor/scan:
- modules/msisensor/scan/**
- tests/modules/msisensor/scan/**
mtnucratio:
- modules/mtnucratio/**
- tests/modules/mtnucratio/**
multiqc:
- modules/fastqc/**
- modules/multiqc/**
- tests/modules/multiqc/**
2021-11-15 15:53:41 +00:00
mummer:
- modules/mummer/**
- tests/modules/mummer/**
muscle:
- modules/muscle/**
- tests/modules/muscle/**
nanolyse:
- modules/nanolyse/**
- tests/modules/nanolyse/**
nanoplot:
- modules/nanoplot/**
- tests/modules/nanoplot/**
ncbigenomedownload:
- modules/ncbigenomedownload/**
- tests/modules/ncbigenomedownload/**
nextclade/datasetget:
- modules/nextclade/datasetget/**
- tests/modules/nextclade/datasetget/**
nextclade/run:
- modules/nextclade/run/**
- tests/modules/nextclade/run/**
ngmaster:
- modules/ngmaster/**
- tests/modules/ngmaster/**
nucmer:
- modules/nucmer/**
- tests/modules/nucmer/**
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/**
paraclu:
- modules/paraclu/**
- tests/modules/paraclu/**
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/**
peddy:
- modules/peddy/**
- tests/modules/peddy/**
phyloflash:
- modules/phyloflash/**
- tests/modules/phyloflash/**
picard/collecthsmetrics:
- modules/picard/collecthsmetrics/**
- tests/modules/picard/collecthsmetrics/**
picard/collectmultiplemetrics:
- modules/picard/collectmultiplemetrics/**
- tests/modules/picard/collectmultiplemetrics/**
picard/collectwgsmetrics:
- modules/picard/collectwgsmetrics/**
- tests/modules/picard/collectwgsmetrics/**
picard/filtersamreads:
- modules/picard/filtersamreads/**
- tests/modules/picard/filtersamreads/**
picard/markduplicates:
- modules/picard/markduplicates/**
- tests/modules/picard/markduplicates/**
picard/mergesamfiles:
- modules/picard/mergesamfiles/**
- tests/modules/picard/mergesamfiles/**
picard/sortsam:
- modules/picard/sortsam/**
- tests/modules/picard/sortsam/**
pirate:
- modules/pirate/**
- tests/modules/pirate/**
plasmidid:
- modules/plasmidid/**
- tests/modules/plasmidid/**
plink/extract:
- modules/plink/extract/**
- tests/modules/plink/extract/**
plink/vcf:
- modules/plink/vcf/**
- tests/modules/plink/vcf/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
plink2/vcf:
- modules/plink2/vcf/**
- tests/modules/plink2/vcf/**
add new module pmdtools/filter #847 (#963) * commit but won't be used because pmdtools should have a submodule * added submodule pmdtools/filter * removed pmdtools module created before deciding to design two submodules * oops forgot to remove a TODO * removed white space meta.yml, removed v in version and manually added submodule /filter to test * Update pytest_modules.yml * Update main.nf added split_cpus for multi-tools module resources * Update test.yml added .pmd extension to match modules/ main.nf * Update test.yml update md5sum * Update singularity and docker build in main.nf From build 4 to 5 in order to match the conda one * Update modules/pmdtools/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pmdtools/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf adding samtools version we need both pmdtools and samtools versions * Update main.nf remove .pmd extension * Update test.yml md5sum Because file extension changed Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2021-11-13 15:09:14 +00:00
pmdtools/filter:
- modules/pmdtools/filter/**
- tests/modules/pmdtools/filter/**
porechop:
- modules/porechop/**
- tests/modules/porechop/**
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/**
pydamage/analyze:
- modules/pydamage/analyze/**
- tests/modules/pydamage/analyze/**
pydamage/filter:
- modules/pydamage/filter/**
- tests/modules/pydamage/filter/**
qcat:
- modules/qcat/**
- tests/modules/qcat/**
qualimap/bamqc:
- modules/qualimap/bamqc/**
- tests/modules/qualimap/bamqc/**
quast:
- modules/quast/**
- tests/modules/quast/**
racon:
- modules/racon/**
- tests/modules/racon/**
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/**
roary:
- modules/roary/**
- tests/modules/roary/**
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/**
rseqc/tin:
- modules/rseqc/tin/**
- tests/modules/rseqc/tin/**
salmon/index:
- modules/salmon/index/**
- tests/modules/salmon/index/**
salmon/quant:
- modules/salmon/quant/**
- tests/modules/salmon/quant/**
samblaster:
- modules/samblaster/**
- tests/modules/samblaster/**
samtools/ampliconclip:
- modules/samtools/ampliconclip/**
- tests/modules/samtools/ampliconclip/**
samtools/bam2fq:
- modules/samtools/bam2fq/**
- tests/modules/samtools/bam2fq/**
samtools/depth:
- modules/samtools/depth/**
- tests/modules/samtools/depth/**
samtools/faidx:
- modules/samtools/faidx/**
- tests/modules/samtools/faidx/**
samtools/fastq:
- modules/samtools/fastq/**
- tests/modules/samtools/fastq/**
samtools/fixmate:
- modules/samtools/fixmate/**
- tests/modules/samtools/fixmate/**
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/**
scoary:
- modules/scoary/**
- tests/modules/scoary/**
seacr/callpeak:
- modules/seacr/callpeak/**
- tests/modules/seacr/callpeak/**
seqkit/split2:
- modules/seqkit/split2/**
- tests/modules/seqkit/split2/**
Update all modules to new NF DSL2 syntax (#1099) * Add comment line for consistency * Remove all functions.nf * Remove include functions.nf and publishDir options * Replace options.args3 with task.ext.args3 - 3 modules * Replace options.args3 with task.ext.args3 - 17 modules * Replace {task.cpus} with task.cpus * Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with * Add def args = task.ext.args line to all modules in script section * Replace options.args with args and args_list * Initialise args2 and args3 properly * Replace container syntax * Revert container changes for cellranger/mkref * Replace getProcessName in all modules * Replace getSoftwareName in all modules * Unify modules using VERSION variable * Replae options.suffix with task.ext.suffix * Remove NF version restriction for CI * Bump NF version in README * Replace task.process.tokenize logic with task.process * Minor tweaks to unify syntax in tests main.nf * Add a separate nextflow.config for each module * Transfer remaining module options to nextflow.config * Remove addParams from tests main.nf * Remove TODO statements * Use -c to import module specific config * Bump NF version to 21.10.3 * Fix tests for artic/minion * Fix broken publishDir syntax * Standardise and fix obvious failing module tests * Remove kronatools to krona * Comment out tags in subworkflow test.yml * Fix failing module tests * Add consistent indentation to nextflow.config * Comment out subworklow definitions * Fix kallistobustools/ref * Fix rmarkdownnotebook * Fix jupyternotebook * Quote task.process * Add plink2/vcf to pytest_modules.yml * Remove NF_CORE_MODULES_TEST from pytest CI * Fix more tests * Move bacteroides_fragilis to prokaryotes folder * Fix cooler merge tests * Fix kallistobustools/count tests * Fix kallistobustools/ref tests * Update test_10x_1_fastq_gz file for kallistobustools/count tests * Fix bcftools/query tests * Fix delly/call tests * Fix cooler/zoomify tests * Fix csvtk/split tests * Fix gatk4/intervallisttools tests * Fix gatk4/variantfiltration * Fix pydamage/filter tests * Fix test data for unicycler * Fix gstama/collapse module * Fix leehom tests * Fix metaphlan3 tests * Fix pairtools/select tests * Update nextflow.config * Update nextflow.config * feat: update syntax * Fix arriba tests * Fix more failing tests * Update test syntax * Remove comments from tests nextflow.config * Apply suggestions from code review * Fix kallistobustools/count module * Update dumpsoftwareversions module * Update custom/dumpsoftwareversions * Add args2 to untar module * Update leftover modules * Remove last remaining addParams Co-authored-by: JoseEspinosa <kadomu@gmail.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
2021-11-26 07:58:40 +00:00
seqsero2:
- modules/seqsero2/**
- tests/modules/seqsero2/**
seqtk/mergepe:
- modules/seqtk/mergepe/**
- tests/modules/seqtk/mergepe/**
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/**
snpdists:
- modules/snpdists/**
- tests/modules/snpdists/**
snpeff:
- modules/snpeff/**
- tests/modules/snpeff/**
snpsift/split:
- modules/snpsift/split/**
- tests/modules/snpsift/split/**
snpsites:
- modules/snpsites/**
- tests/modules/snpsites/**
spades:
- modules/spades/**
- tests/modules/spades/**
spatyper:
- modules/spatyper/**
- tests/modules/spatyper/**
sratools/fasterqdump:
- modules/sratools/fasterqdump/**
- tests/modules/sratools/fasterqdump/**
sratools/prefetch:
- modules/sratools/prefetch/**
- tests/modules/sratools/prefetch/**
staphopiasccmec:
- modules/staphopiasccmec/**
- tests/modules/staphopiasccmec/**
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/**
strelka/somatic:
- modules/strelka/somatic/**
- tests/modules/strelka/somatic/**
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/**
tbprofiler/profile:
- modules/tbprofiler/profile/**
- tests/modules/tbprofiler/profile/**
tiddit/cov:
- modules/tiddit/cov/**
- tests/modules/tiddit/cov/**
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/**
ucsc/liftover:
- modules/ucsc/liftover/**
- tests/modules/ucsc/liftover/**
ucsc/wigtobigwig:
- modules/ucsc/wigtobigwig/**
- tests/modules/ucsc/wigtobigwig/**
ultra/pipeline:
- modules/ultra/pipeline/**
- tests/modules/ultra/pipeline/**
unicycler:
- modules/unicycler/**
- tests/modules/unicycler/**
untar:
- modules/untar/**
- tests/modules/untar/**
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/**
vcfanno:
- modules/vcfanno/**
- tests/modules/vcfanno/**
vcflib/vcfuniq:
- modules/vcflib/vcfuniq/**
- tests/modules/vcflib/vcfuniq/**
vcftools:
- modules/vcftools/**
- tests/modules/vcftools/**
yara/index:
- modules/yara/index/**
- tests/modules/yara/index/**
yara/mapper:
- modules/yara/mapper/**
- tests/modules/yara/mapper/**