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nf-core_modules/tests/config/pytest_software.yml

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Add abacas module (#431) * Add abacas module * Add test for abacas module * Add Harshil to authorship * Updating test with the data uploaded to nf-core/datasets * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 14:37:08 +00:00
abacas:
- software/abacas/**
- tests/software/abacas/**
new module: AdapterRemoval (#309) * add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
adapterremoval:
- software/adapterremoval/**
- tests/software/adapterremoval/**
Add alleleCounter module (#313) * Add allelecount module * Add bed file input * Added bai file * Changed conda version * Update main.nf * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Add allelecount module * Add bed file input * Added bai file * Changed conda version * Update main.nf * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Update pytest_software.yml * Remove newline * Fix pytest_software.yml * Update pytest_software.yml Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-03-23 13:37:53 +00:00
allelecounter:
- software/allelecounter/**
- tests/software/allelecounter/**
Add artic guppyplex (#455) * Adding artic guppyplex module * Adding guppyplex tests * Fix tests * Correcting typo * Fix lint * Fix test * Missing description * Missing descriptions * Update functions to last version as suggested * Bump newest version of nanoplot
2021-04-27 14:57:34 +00:00
artic/guppyplex:
- software/artic/guppyplex/**
- tests/software/artic/guppyplex/**
Add artic minion (#486) * Add artic minion module * Add fast5 to test data configuration * Add test for artic minion
2021-05-07 15:37:35 +00:00
artic/minion:
- software/artic/minion/**
- tests/software/artic/minion/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bandage/image:
Address review comments
2021-02-04 18:10:54 +00:00
- software/bandage/image/**
- tests/software/bandage/image/**
Bbmap/bbduk (#487) * bbmap/bbduk module created * created bbmap/bbduk module * updated main.nf * changed test.yml tags * removed whitespaces * Adjusted main.nf spacing * whitespace, tags * fix optional files, tags, tidy code * fix suffix * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-10 10:45:52 +00:00
bbmap/bbduk:
- software/bbmap/bbduk/**
- tests/software/bbmap/bbduk/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bcftools/consensus:
Update .github/filters.yml
2021-02-08 21:48:21 +00:00
- software/bcftools/consensus/**
Fixing trailing slashes in .github/filters.yml
2021-02-09 17:16:16 +00:00
- tests/software/bcftools/consensus/**
Adding again bcftools modules to filters after solving conflict
2021-02-08 17:10:50 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bcftools/filter:
Fix copy/paste error :P
2021-02-08 20:57:31 +00:00
- software/bcftools/filter/**
Fixing trailing slashes in .github/filters.yml
2021-02-09 17:16:16 +00:00
- tests/software/bcftools/filter/**
Adding again bcftools modules to filters after solving conflict
2021-02-08 17:10:50 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bcftools/isec:
Fix copy/paste error :P
2021-02-08 20:57:31 +00:00
- software/bcftools/isec/**
Fixing trailing slashes in .github/filters.yml
2021-02-09 17:16:16 +00:00
- tests/software/bcftools/isec/**
Adding again bcftools modules to filters after solving conflict
2021-02-08 17:10:50 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bcftools/merge:
Add bcftools merge module
2021-02-12 23:08:57 +00:00
- software/bcftools/merge/**
- tests/software/bcftools/merge/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bcftools/mpileup:
Add tests for bcftools-mpileup
2021-02-23 18:05:57 +00:00
- software/bcftools/mpileup/**
- tests/software/bcftools/mpileup/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bcftools/stats:
Fix copy/paste error :P
2021-02-08 20:57:31 +00:00
- software/bcftools/stats/**
Fixing trailing slashes in .github/filters.yml
2021-02-09 17:16:16 +00:00
- tests/software/bcftools/stats/**
Adding again bcftools modules to filters after solving conflict
2021-02-08 17:10:50 +00:00
add bedtools bamtobed module (from nanoseq modules) (#466) * add bedtools bamtobed module * fix erros * fix linting problem
2021-04-30 12:20:31 +00:00
bedtools/bamtobed:
- software/bedtools/bamtobed/**
- tests/software/bedtools/bamtobed/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bedtools/complement:
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
- software/bedtools/complement/**
- tests/software/bedtools/complement/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bedtools/genomecov:
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
- software/bedtools/genomecov/**
- tests/software/bedtools/genomecov/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bedtools/getfasta:
Add bedtools getfasta module
2021-02-09 16:56:51 +00:00
- software/bedtools/getfasta/**
- tests/software/bedtools/getfasta/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bedtools/intersect:
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
- software/bedtools/intersect/**
- tests/software/bedtools/intersect/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bedtools/maskfasta:
Add bedtools maskfasta module
2021-02-08 22:41:10 +00:00
- software/bedtools/maskfasta/**
- tests/software/bedtools/maskfasta/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bedtools/merge:
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
- software/bedtools/merge/**
- tests/software/bedtools/merge/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bedtools/slop:
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
- software/bedtools/slop/**
- tests/software/bedtools/slop/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bedtools/sort:
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
- software/bedtools/sort/**
- tests/software/bedtools/sort/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bismark/align:
add bismark/report (#297) * add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/report * fix test filepaths * remove mysterious index files
2021-03-22 12:38:08 +00:00
- software/bismark/align/**
bismark: remove underscores from process names (#303) * sanitize process names no underscores allowed * remove underscores from process names
2021-03-22 16:46:11 +00:00
- software/bismark/genomepreparation/**
add bismark/report (#297) * add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/report * fix test filepaths * remove mysterious index files
2021-03-22 12:38:08 +00:00
- tests/software/bismark/align/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bismark/deduplicate:
add bismark/deduplicate + tests
2021-02-23 17:02:16 +00:00
- software/bismark/deduplicate/**
- tests/software/bismark/deduplicate/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bismark/genomepreparation:
bismark: remove underscores from process names (#303) * sanitize process names no underscores allowed * remove underscores from process names
2021-03-22 16:46:11 +00:00
- software/bismark/genomepreparation/**
- tests/software/bismark/genomepreparation/**
add bismark/genome_preparation + tests
2021-02-18 09:56:36 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bismark/methylationextractor:
bismark: remove underscores from process names (#303) * sanitize process names no underscores allowed * remove underscores from process names
2021-03-22 16:46:11 +00:00
- software/bismark/methylationextractor/**
- software/bismark/genomepreparation/**
- tests/software/bismark/methylationextractor/**
add bismark/methylation_extractor (#274) * add bismark/methylation_extractor * add tests for bismark/methylation_extractor * bismark/methylation_extractor: add genome_preparation to filters * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * remove params from meta.yml * pytest: remove md5sum checks for gzipped output gzip stores timestamps in the file header, so the checksum will be different each time Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-20 23:54:42 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bismark/report:
bismark: remove underscores from process names (#303) * sanitize process names no underscores allowed * remove underscores from process names
2021-03-22 16:46:11 +00:00
- software/bismark/genomepreparation/**
add bismark/report (#297) * add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/report * fix test filepaths * remove mysterious index files
2021-03-22 12:38:08 +00:00
- software/bismark/align/**
- software/bismark/deduplicate/**
bismark: remove underscores from process names (#303) * sanitize process names no underscores allowed * remove underscores from process names
2021-03-22 16:46:11 +00:00
- software/bismark/methylationextractor/**
add bismark/report (#297) * add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/report * fix test filepaths * remove mysterious index files
2021-03-22 12:38:08 +00:00
- software/bismark/report/**
- tests/software/bismark/report/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bismark/summary:
bismark: remove underscores from process names (#303) * sanitize process names no underscores allowed * remove underscores from process names
2021-03-22 16:46:11 +00:00
- software/bismark/genomepreparation/**
add bismark/summary (#295) * add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/summary * remove md5sum check for bismark_summary_report.html it contains a timestamp * fix tests * update meta.yml * remove mysterious index files
2021-03-22 13:58:54 +00:00
- software/bismark/align/**
- software/bismark/deduplicate/**
bismark: remove underscores from process names (#303) * sanitize process names no underscores allowed * remove underscores from process names
2021-03-22 16:46:11 +00:00
- software/bismark/methylationextractor/**
add bismark/summary (#295) * add bismark/align module * bismark/align: add tests * bismark/align: update meta.yml * bismark/align: skip checksum for alignment logs they contain timestamps * bismark/align: restore correct checksum caused some mixup in the last commit * bismark/align: add genome_preparation to filters * Fix conda version pin * change options to be a global var * remove params from meta.yml * add bismark/summary * remove md5sum check for bismark_summary_report.html it contains a timestamp * fix tests * update meta.yml * remove mysterious index files
2021-03-22 13:58:54 +00:00
- software/bismark/summary/**
- tests/software/bismark/summary/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
blast/blastn:
new module: AdapterRemoval (#309) * add adapterremoval module * fix indentations * switch to process_medium * update docker tests * remove duplicated entry * fix line ending * Update software/adapterremoval/main.nf * Update software/adapterremoval/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
- software/blast/blastn/**
- tests/software/blast/blastn/**
Add gatk4/applybqsr (#331) * Add applybqsr module * Solve problem in functions.nf * Add to pytest
2021-03-23 13:15:26 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
blast/makeblastdb:
add bismark/methylation_extractor (#274) * add bismark/methylation_extractor * add tests for bismark/methylation_extractor * bismark/methylation_extractor: add genome_preparation to filters * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * remove params from meta.yml * pytest: remove md5sum checks for gzipped output gzip stores timestamps in the file header, so the checksum will be different each time Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-20 23:54:42 +00:00
- software/blast/makeblastdb/**
- tests/software/blast/makeblastdb/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bowtie/align:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/bowtie/align/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
- software/bowtie/build/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/bowtie/align/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bowtie/build:
add picard_collectwgsmetrics (#304) * Added new module picard/collectwgsmetrics. * Removed unused outputs from meta.yml * Added version.txt file back to meta.yml * Updated test.yml * Removed md5sum from test.yaml and added contain tests. * Update functions.nf Fixed missing newline formatting. * Update main.nf Fixed missing newline formatting. * style(picard): Remove trailing whitespace Co-authored-by: Kevin Menden <kevin.menden@t-online.de> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-22 16:05:59 +00:00
- software/bowtie/build/**
- tests/software/bowtie/build_test/**
Update filters paths
2021-02-03 16:04:43 +00:00
add rapidnj module (#421) * add rapidnj module * remove trailing whitespace * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 12:04:54 +00:00
bowtie2/align:
- software/bowtie2/align/**
- software/bowtie2/build/**
- tests/software/bowtie2/align/**
bowtie2/build:
- software/bowtie2/build/**
- tests/software/bowtie2/build_test/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bwa/index:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/bwa/index/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/bwa/index/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bwa/mem:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/bwa/mem/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/bwa/mem/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bwamem2/index:
chores: update filters.yml
2021-02-12 12:53:49 +00:00
- software/bwamem2/index/**
- tests/software/bwamem2/index/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bwamem2/mem:
chores: update filters.yml
2021-02-12 12:53:49 +00:00
- software/bwamem2/mem/**
- tests/software/bwamem2/mem/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bwameth/align:
add bwameth/align module + tests
2021-02-17 17:23:11 +00:00
- software/bwameth/align/**
- tests/software/bwameth/align/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
bwameth/index:
add bwameth/index module + test
2021-02-17 17:03:48 +00:00
- software/bwameth/index/**
- tests/software/bwameth/index/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
cat/fastq:
Add cat fastq module
2021-02-12 16:22:07 +00:00
- software/cat/fastq/**
- tests/software/cat/fastq/**
cnvkit module (#173) * Normal bam file added * Normal bam.bai file added * Tumour bam bai files added * human dir added * annotation dir added * cnvkit dir added * cnvkit dir added * Update software/cnvkit/main.nf Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> * Update software/cnvkit/main.nf Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> * Update software/cnvkit/main.nf Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> * changed input filenames * edited main.nf * edited main.nf * edited meta.nf * edited test.yml * filters.yml * edited main * edited main * edited meta * edited meta * edited main * removed unwanted lines * edited the path to the main.nf * removed function.nf * added functions.nf * deleted 2 workflows and craeted a common workflow * deleted paths for 2 workflows and created paths for a common workflow * Deleted annotation dir * deleted params.modules * Edited meta.with_normal * deleted normal_280_sub_chr21.bam * deleted normal_280_sub_chr21.bam.bai * deleted tumour_278_sub_chr21.bam * deleted tumour_278_sub_chr21.bam.bai * Edited input and script parts * Edited input part * Added * Edited args * Edited script * Edited input * Changed annotation to annotationfile * Changed description of the tool * edited singularuty container * edited input * line 44 removed trailing whitespace * Edited addParams * Deleted pdf output * Deleted pdf output * edited the path to main.nf * edited path to the main.nf * Added docker image version * Removed extra ../ * added md5sums * added md5sums * Update software/cnvkit/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/cnvkit/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Edited the script * Edited the input * Edited main.nf * Edited main.nf * edited md5sum for reference.cnn * removed human fasta * removed human fasta.fai * added GRCh38 fasta * added GRCh38 fasta.fai * added hg19 fasta.fai * added hg19 fasta * Edited fasta file name * Edited bed file names and md5sums * Edited md5sums * edited the input and script section * edited input section * added targetfile * changed the files * changed the output files * added bam files * added bam files * remove files * added md5sums * replace file * added files * edited tests/software/cnvkit files * edited tests/software/cnvkit files * edited authors list * removed files * added files * added files * added files * added files * added file * added file * added file * added file * edited files * edited files * edited files * edited files * edited files * edited files * added new module * added new module * edited files * edited file * edited file * edited file * removed files Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com> Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 22:27:30 +00:00
cnvkit:
- software/cnvkit/**
- tests/software/cnvkit/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
cutadapt:
- software/cutadapt/**
- tests/software/cutadapt/**
Finish deeptools modules (#442) * Adding bigWig and deeptools computeMatrix files to config * Adding meta.yml for deeptools modules * Add test for deeptools modules * Fixing and reordering tags * Fixing conda test that worked in local... * Apply suggestions from code review * Changing bigwig file pattern to include bigwig extension * Saving after last change is a good practice Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 20:48:43 +00:00
deeptools/computematrix:
- software/deeptools/computematrix/**
- tests/software/deeptools/computematrix/**
deeptools/plotfingerprint:
- software/deeptools/plotfingerprint/**
- tests/software/deeptools/plotfingerprint/**
deeptools/plotheatmap:
- software/deeptools/plotheatmap/**
- tests/software/deeptools/plotheatmap/**
deeptools/plotprofile:
- software/deeptools/plotprofile/**
- tests/software/deeptools/plotprofile/**
Update dsh-bio modules to version 2.0.4 (#482) * Update dsh-bio modules to version 2.0.4 * update docker tag * update md5 checksums * Update software/dshbio/filtergff3/main.nf * Update software/dshbio/splitgff3/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-04 13:28:44 +00:00
dshbio/filterbed:
- software/dshbio/filterbed/**
- tests/software/dshbio/filterbed/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
Update dsh-bio modules to version 2.0.4 (#482) * Update dsh-bio modules to version 2.0.4 * update docker tag * update md5 checksums * Update software/dshbio/filtergff3/main.nf * Update software/dshbio/splitgff3/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-04 13:28:44 +00:00
dshbio/filtergff3:
- software/dshbio/filtergff3/**
- tests/software/dshbio/filtergff3/**
dshbio/splitbed:
- software/dshbio/splitbed/**
- tests/software/dshbio/splitbed/**
dshbio/splitgff3:
- software/dshbio/splitgff3/**
- tests/software/dshbio/splitgff3/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
fastp:
- software/fastp/**
- tests/software/fastp/**
ci: Use paths-filter to make one CI test
2021-01-24 04:55:07 +00:00
fastqc:
- software/fastqc/**
- tests/software/fastqc/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
adding fasttree module (#412) * adding fasttree module * correct trailing whitespace * using sarscov2 as a test dir * remove TODO * update test data naming * further test data naming updates * remove options in favour of $options.args * ensure non standard exit codes don't cause an issue * update md5sum
2021-04-08 17:15:23 +00:00
fasttree:
- software/fasttree/**
- tests/software/fasttree/**
Added kallistobustools/ref (#408) * Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me * Removed trailing whitespace line 29 * Moved workflow from meta to options. * Update main.nf * Forgot to remove previous testing input channel for workflow. * Apply suggestions from code review Applied changes suggested by @drpatelh Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added gtf to meta.yml. * Apply suggestions from code review Adding @drpatelh suggested changes. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Moved workflow to input value. Fixed tests. * Update tests/software/kallistobustools/ref/test.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 08:41:41 +00:00
fgbio/callmolecularconsensusreads:
New modules: Fgbio callmolecularconsensusreads and sortbam (#352) * Added fgbio callmolecularconsensusreads and sortbam modules * Fixed naming issue in meta.yml * fix: test.yml and config lint * Revert "fix: test.yml and config lint" This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail. * style: Fix test names * style: Remove trailing whitespace * fixed test.yml * fix: test data in sortbam * fix: data format * fix: test data for callmolecularconsensusreads * Corrected with updated test data * Apply suggestions from code review Applied changes from code review, mainly syntactical changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-28 19:38:50 +00:00
- software/fgbio/callmolecularconsensusreads/**
- tests/software/fgbio/callmolecularconsensusreads/**
Added kallistobustools/ref (#408) * Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me * Removed trailing whitespace line 29 * Moved workflow from meta to options. * Update main.nf * Forgot to remove previous testing input channel for workflow. * Apply suggestions from code review Applied changes suggested by @drpatelh Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added gtf to meta.yml. * Apply suggestions from code review Adding @drpatelh suggested changes. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Moved workflow to input value. Fixed tests. * Update tests/software/kallistobustools/ref/test.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 08:41:41 +00:00
fgbio/sortbam:
New modules: Fgbio callmolecularconsensusreads and sortbam (#352) * Added fgbio callmolecularconsensusreads and sortbam modules * Fixed naming issue in meta.yml * fix: test.yml and config lint * Revert "fix: test.yml and config lint" This reverts commit 0453bc3a8dc3dab6997442a4349ee2241adcc380, which caused the sortbam tests to fail. * style: Fix test names * style: Remove trailing whitespace * fixed test.yml * fix: test data in sortbam * fix: data format * fix: test data for callmolecularconsensusreads * Corrected with updated test data * Apply suggestions from code review Applied changes from code review, mainly syntactical changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Sruthi Suresh <sps180004@ganymede.utdallas.edu> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-28 19:38:50 +00:00
- software/fgbio/sortbam/**
- tests/software/fgbio/sortbam/**
add flash module (#341) * add flash module * remove todo * run tests Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 05:05:45 +00:00
flash:
- software/flash/**
- tests/software/flash/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/applybqsr:
Add gatk4/applybqsr (#331) * Add applybqsr module * Solve problem in functions.nf * Add to pytest
2021-03-23 13:15:26 +00:00
- software/gatk4/applybqsr/**
- tests/software/gatk4/applybqsr/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/baserecalibrator:
Add gatk4/baserecalibrator (#327) * Add gatk4 BaseRecalibrator * Solve format in main.nf * Correct functions * Add pytest
2021-03-23 17:32:37 +00:00
- software/gatk4/baserecalibrator/**
- tests/software/gatk4/baserecalibrator/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/bedtointervallist:
Rename gatk/createsequencedictionary -> gatk4/createsequencedictionary (#260) * fix: update and sort filters * fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary
2021-03-08 13:45:46 +00:00
- software/gatk4/bedtointervallist/**
- tests/software/gatk4/bedtointervallist/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/createsequencedictionary:
Rename gatk/createsequencedictionary -> gatk4/createsequencedictionary (#260) * fix: update and sort filters * fix: rename gatk/createsequencedictionary -> gatk4/createsequencedictionary
2021-03-08 13:45:46 +00:00
- software/gatk4/createsequencedictionary/**
- tests/software/gatk4/createsequencedictionary/**
chores: add gatk/createsequencedictionary module
2021-02-16 12:40:06 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/fastqtosam:
add gatk4/fastqtosam #198 (#311) * Inital nf-core create * remove TODO comments, input and output files defined * add get version in script * added flow control for single/paired end data * added script main commands * removed completed TODO messages * removed completed TODO messages * added software info * added input reads description * added output description * added description and keywords * added single end test * added paired end test * fixed sample name flag * fixed reverse read variable * added test yaml * update for pytest_software * order in pytest_software was different * replaced functions.nf with copy from another module * simplify read command line Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 18:26:02 +00:00
- software/gatk4/fastqtosam/**
- tests/software/gatk4/fastqtosam/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/haplotypecaller:
modify test path - module gatk4 + added new module gatk4/haplotypecaller (#382) * new module: samtools/fastq * solve conflict: pytest_software.yml * solve linting conflicts * solved EditorConfig linting problem * Module samtools/fastq: * output compressed fastq.gz file(s) * add if conditionals for single/paired reads * samtools/fastq: modified test.yml * samtools/fastq: modified main.nf to avoid duplicated part of the script section * fix README.md * modify test path gatk4 * fix config * Add new module gatk4/haplotypecaller * solve check issues * fix test.yml file * fix test.yml gz.tbi * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/haplotypecaller/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/haplotypecaller/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: suzannejin <suzanne.jin@crg.eu> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 11:46:46 +00:00
- software/gatk4/haplotypecaller/**
- tests/software/gatk4/haplotypecaller/**
New last/split module to find split alignments. (#511) * New last/split module to find split alignments. The `last-split` tool distributed with [LAST](https://gitlab.com/mcfrith/last) finds split or spliced alignments in a MAF file that is produced with, for example, LAST `lastal` command. This new module is part of the work discribed in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Update software/last/split/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-24 19:15:57 +00:00
gatk4/intervallisttools:
- software/gatk4/intervallisttools/**
- tests/software/gatk4/intervallisttools/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/markduplicates:
PR for sequenzautils/bam2seqz (#395) * added files * edited files * removed file * README.md edited Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-04-01 05:08:27 +00:00
- software/gatk4/markduplicates/**
- tests/software/gatk4/markduplicates/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/mergebamalignment:
Add spades module (#277) * Add spades module * Reorder gatk4 modules alphabetically * Update software/spades/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:48:38 +00:00
- software/gatk4/mergebamalignment/**
- tests/software/gatk4/mergebamalignment/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/mergevcfs:
working test
2021-02-19 12:36:42 +00:00
- software/gatk4/mergevcfs/**
- tests/software/gatk4/mergevcfs/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/revertsam:
added gatk4 revertsam
2021-02-22 14:21:39 +00:00
- software/gatk4/revertsam/**
- tests/software/gatk4/revertsam/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/samtofastq:
added gatk4 SamToFastq
2021-02-19 11:41:29 +00:00
- software/gatk4/samtofastq/**
- tests/software/gatk4/samtofastq/**
add gatk4 bedtointervallist
2021-02-19 10:26:31 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/splitncigarreads:
added entry to filters.yml
2021-02-22 12:36:49 +00:00
- software/gatk4/splitncigarreads/**
- tests/software/gatk4/splitncigarreads/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
gatk4/variantfiltration:
Add spades module (#277) * Add spades module * Reorder gatk4 modules alphabetically * Update software/spades/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:48:38 +00:00
- software/gatk4/variantfiltration/**
- tests/software/gatk4/variantfiltration/**
add genmap/mappability (#509) * add genmap/mappability * Add index module. Remove -w parameter from mappability module. * change the output of genmap/index * fix the lint error which can not handle stageAs. * Apply suggestions from code review * Update main.nf * Update test.yml * Update main.nf * Update test.yml * Update tests/software/genmap/mappability/main.nf * Update software/genmap/mappability/main.nf * Update software/genmap/mappability/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 21:12:10 +00:00
genmap/index:
- software/genmap/index/**
- tests/software/genmap/index/**
genmap/mappability:
- software/genmap/mappability/**
- tests/software/genmap/mappability/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
gffread:
- software/gffread/**
- tests/software/gffread/**
add graphmap index and align modules (from nanoseq modules) (#468) * add graphmap index module * add graphmap2/index * add graohmap2 align module * remove graphmap2 align md5sum
2021-04-30 12:18:58 +00:00
graphmap2/align:
- software/graphmap2/align/**
- tests/software/graphmap2/align/**
graphmap2/index:
- software/graphmap2/index/**
- tests/software/graphmap2/index/**
new module: gubbins (#377) * new gubbins module * new gubbins module * new gubbins module * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-07 15:31:24 +00:00
gubbins:
- software/gubbins/**
- tests/software/gubbins/**
Add gunzip module
2021-02-09 09:05:55 +00:00
gunzip:
- software/gunzip/**
- tests/software/gunzip/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
hisat2/align:
Add tests for hisat2 (#366) * initial commit hisat2/build * initial commit hisat2/build * changed names for hisat2 * fixed directory structure and args * added splice site test data * added splice site inputs * replaced list with individual args * fixed removed commas * added test yml file * updated hisat2 conda version * added meta.yml * added meta.yml description * added meta.yml inputs * added meta.yml outputs * update conda version for hisat2 * removed trailing whitespace meta.yml * fixed version number for containers * added test data to test config * updated for new test logic * fix pytest issue? * fix pytest issue * fixed wrong tool in meta.yaml * updated tets.yaml name * handle build bug for testing * handle build bug for testing in yaml * moved test folder to fix build bug * use old hisat2 version to avoid conda giving inconsistent md5sum * initial commit * removed temp file * added meta yaml * add to pytest * added tests * added test yml * add align meta yaml * add hisat2 align to pytest * remove need for splice data by calling process * add hisat2 align se test * add hisat2 align pe test * update names hisat2 align * update software pytest for using mutiple modules * remove splice site test data since using module instead * remove splice site from config since using module instead * fixed extra brace * added hisat2 align test.yml * removed md5sum for bam files * updated build md5sums * Apply suggestions from code review Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 21:08:46 +00:00
- software/hisat2/align/**
- software/hisat2/build/**
- software/hisat2/extractsplicesites/**
- tests/software/hisat2/align/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
hisat2/build:
Add tests for hisat2 (#366) * initial commit hisat2/build * initial commit hisat2/build * changed names for hisat2 * fixed directory structure and args * added splice site test data * added splice site inputs * replaced list with individual args * fixed removed commas * added test yml file * updated hisat2 conda version * added meta.yml * added meta.yml description * added meta.yml inputs * added meta.yml outputs * update conda version for hisat2 * removed trailing whitespace meta.yml * fixed version number for containers * added test data to test config * updated for new test logic * fix pytest issue? * fix pytest issue * fixed wrong tool in meta.yaml * updated tets.yaml name * handle build bug for testing * handle build bug for testing in yaml * moved test folder to fix build bug * use old hisat2 version to avoid conda giving inconsistent md5sum * initial commit * removed temp file * added meta yaml * add to pytest * added tests * added test yml * add align meta yaml * add hisat2 align to pytest * remove need for splice data by calling process * add hisat2 align se test * add hisat2 align pe test * update names hisat2 align * update software pytest for using mutiple modules * remove splice site test data since using module instead * remove splice site from config since using module instead * fixed extra brace * added hisat2 align test.yml * removed md5sum for bam files * updated build md5sums * Apply suggestions from code review Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 21:08:46 +00:00
- software/hisat2/build/**
- software/hisat2/extractsplicesites/**
- tests/software/hisat2/build_test/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
hisat2/extractsplicesites:
Add tests for hisat2 (#366) * initial commit hisat2/build * initial commit hisat2/build * changed names for hisat2 * fixed directory structure and args * added splice site test data * added splice site inputs * replaced list with individual args * fixed removed commas * added test yml file * updated hisat2 conda version * added meta.yml * added meta.yml description * added meta.yml inputs * added meta.yml outputs * update conda version for hisat2 * removed trailing whitespace meta.yml * fixed version number for containers * added test data to test config * updated for new test logic * fix pytest issue? * fix pytest issue * fixed wrong tool in meta.yaml * updated tets.yaml name * handle build bug for testing * handle build bug for testing in yaml * moved test folder to fix build bug * use old hisat2 version to avoid conda giving inconsistent md5sum * initial commit * removed temp file * added meta yaml * add to pytest * added tests * added test yml * add align meta yaml * add hisat2 align to pytest * remove need for splice data by calling process * add hisat2 align se test * add hisat2 align pe test * update names hisat2 align * update software pytest for using mutiple modules * remove splice site test data since using module instead * remove splice site from config since using module instead * fixed extra brace * added hisat2 align test.yml * removed md5sum for bam files * updated build md5sums * Apply suggestions from code review Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 21:08:46 +00:00
- software/hisat2/extractsplicesites/**
- tests/software/hisat2/extractsplicesites/**
gatk4 markduplicates (#356) * new module gatk4/markduplicates * add tests * add gatk4_markduplicates entry in pytest_software.yml * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gatk4/markduplicates/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Fix EC lint * Update md5sum Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-26 23:25:40 +00:00
New module to use hmmalign from HMMER to align sequences (#470) * Ignore vim tmp files * Added hmmalign module, not yet tests * Test output * Replaced functions.nf for hmmalign with upstream * Update software/hmmer/hmmalign/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/hmmer/hmmalign/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/hmmer/hmmalign/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/hmmer/hmmalign/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/hmmer/hmmalign/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/hmmer/hmmalign/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/hmmer/hmmalign/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-28 10:21:24 +00:00
hmmer/hmmalign:
- software/hmmer/hmmalign/**
- tests/software/hmmer/hmmalign/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
homer/annotatepeaks:
Homer (#330) * started with homer * added tests for homer annotatepeaks * fix md5 * remove md5 sum
2021-03-23 18:24:54 +00:00
- software/homer/annotatepeaks/**
- tests/software/homer/annotatepeaks/**
add new iqtree module (#427) * add new iqtree module * Resolve suggests after PR review * add newline to functions
2021-04-12 08:45:56 +00:00
iqtree:
- software/iqtree/**
- tests/software/iqtree/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
ivar/consensus:
Add ivar consensus to filter.yml
2021-02-12 18:59:46 +00:00
- software/ivar/consensus/**
- tests/software/ivar/consensus/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
ivar/trim:
Add ivar trim
2021-02-13 00:02:10 +00:00
- software/ivar/trim/**
- tests/software/ivar/trim/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
ivar/variants:
Add ivar variants
2021-02-15 17:28:10 +00:00
- software/ivar/variants/**
- tests/software/ivar/variants/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
kallisto/index:
Add module kallisto/index (#357) * add kallisto index module * update kallisto module * add kallisto module tests * update kallisto index test.yml * update test data paths * fix version * fix kallisto index test yml * remove TODOs * Update software/kallisto/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/kallisto/index/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * output folder instead Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 12:25:39 +00:00
- software/kallisto/index/**
- tests/software/kallisto/index/**
Added kallistobustools/count (#409) * Basic kb-python count functionality for scRNA-seq quantification working. * Added tests and test data for workflow kite. * Removed trailing whitespace * Changed output channels to tuples with meta Based on suggestions by @KevinMenden. * Moved workflow and technology to input variables. Currently create test-yaml file script failes with cryptic message. * Update software/kallistobustools/count/main.nf @KevinMenden fixed wrong path definition Co-authored-by: Kevin Menden <kevin.menden@live.com> * Increased version of kb-python * Updated tests with raw links. * Fixed subtool referencing: kallistobustools/count * Added newline * Update software/kallistobustools/count/main.nf Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-04-30 05:27:17 +00:00
kallistobustools/count:
- software/kallistobustools/count/**
- tests/software/kallistobustools/count/**
Added kallistobustools/ref (#408) * Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me * Removed trailing whitespace line 29 * Moved workflow from meta to options. * Update main.nf * Forgot to remove previous testing input channel for workflow. * Apply suggestions from code review Applied changes suggested by @drpatelh Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added gtf to meta.yml. * Apply suggestions from code review Adding @drpatelh suggested changes. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Moved workflow to input value. Fixed tests. * Update tests/software/kallistobustools/ref/test.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 08:41:41 +00:00
kallistobustools/ref:
- software/kallistobustools/ref/**
- tests/software/kallistobustools/ref/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
kraken2/run:
Add kraken2 run module (#266) * Add kraken2 run module * Add kraken2 run module * Add coronavirus kraken2 db * Adding kraken2 run tests * Update software/kraken2/run/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Fixing files commited by mistake * Remove params for meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:08:06 +00:00
- software/kraken2/run/**
Add kraken2 pigz multi-tool container for compressing output fastq files (#434) * Add kraken2 pigz multi-tool container for compressing output fastq files * Add untar to pytest config * Add untar process to kraken2 tests * Remove unneeded tags
2021-04-12 16:47:34 +00:00
- software/untar/**
Add kraken2 run module (#266) * Add kraken2 run module * Add kraken2 run module * Add coronavirus kraken2 db * Adding kraken2 run tests * Update software/kraken2/run/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Fixing files commited by mistake * Remove params for meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:08:06 +00:00
- tests/software/kraken2/run/**
New last/dotplot module for pairwise similarity plots (#529) * New last/dotplot module for pairwise similarity plots The `last-dotplot` tool takes a pairwise alignment in [MAF](http://genome.ucsc.edu/FAQ/FAQformat.html#format5) format, possibly compressed with gzip, or in a tabular format produced by the `maf-convert` tool, and produces a similarity dot-plot of the two sequences in one of the graphical formats supported by the Python Imaging Library. A the tool guesses the output format by the file extension of the file, which is constructed by the module at run time, I have used the `args2` option to convey this information to the module. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence please ignore lint's version warning). * Update the functions.nf file to the dev branch. https://raw.githubusercontent.com/nf-core/tools/dev/nf_core/module-template/software/functions.nf
2021-06-08 09:13:51 +00:00
last/dotplot:
- software/last/dotplot/**
- tests/software/last/dotplot/**
New last/lastal module to align query sequences on a target index (#510) * New last/lastal to align query sequences on a target index `lastal` is the main program of the [LAST](https://gitlab.com/mcfrith/last) suite. It align query DNA sequences in FASTA or FASTQ format to a target index of DNA or protein sequences. The index is produced by the `lastdb` program (module `last/lastdb`). The score matrix for evaluating the alignment can be chosen among preset ones or computed iteratively by the `last-train` program (module `last/train`). For this reason, the `last/lastal` module proposed here has one input channel containing an optional file, that has to be dummy when not used. The LAST aligner outputs MAF files that can be very large (up to hundreds of gigabytes), therefore this module unconditionally compresses its output with gzip. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Un-hardcode the path to the LAST index. Among multiple alternatives I have chosen the following command to detect the sample name of the index, because it fails in situations where there is no index files in the index folder, and in situations were there are two indexes files in the folder. Not failing would result in feeding garbage information in the INDEX_NAME variable. basename \$(ls $index/*.bck) .bck In case of missing file, a clear error message is given by `ls`. In case of more than one file, the error message of `basename` is more cryptic, unfortunately. (`basename: extra operand ‘.bck’`) Alternatives that do not fail if there is no .bck file: basename $index/*bck .bck find $index -name '*bck' | sed 's/.bck//' Alternatives that do not fail if there are more than one .bck file: basename -s .bck $index/*bck ls $index/*.bck | xargs basename -s .bck find $index -name '*bck' | sed 's/.bck//' Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-25 21:10:48 +00:00
last/lastal:
- software/last/lastal/**
- tests/software/last/lastal/**
New last/lastdb module to index sequences before alignment. (#476) * New last/lastdb module to index sequences before alignment. The `lastdb` command creates a sequence index for the LAST aligner (https://gitlab.com/mcfrith/last). Input can be in FASTA or FASTQ format, and compression is handled automagically. DNA or protein sequences can be indexed. The sequence index is a collection of files sharing the same basename. This module sets the basename to the sample identifier (`$meta.id`) and creates the index in a directory always called `lastdb`. The module's output channel then conveys a copy of the metadata and the path to the `lastdb` directory. Other modules will follow (see Issue #464). The LAST aligner can align proteins to proteins, DNA to DNA and can translate DNA align to proteins. * Remove trailing whitespace. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update as suggested in PR. * Attempt to pass linting. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-02 10:36:31 +00:00
last/lastdb:
- software/last/lastdb/**
- tests/software/last/lastdb/**
New module last/mafswap to reorder sequences in alignments (#500) * New module last/mafswap to reorder sequences in alignments The `maf-swap` tool distributed with [LAST](https://gitlab.com/mcfrith/last) reorders sequences in alignment files in Multiple Alignment Format. When run without command-line arguments, it will swap the target and the query sequences. This is useful when turning a many-to-many alignment into a many-to-one and then a one-to-one alignment in conjunction with the `last-split` command (split, swap, split and swap again). The LAST aligner outputs MAF files, but other tools also use this format. As MAF files can be very large (up to hundreds of gigabytes), the module expects its input to be compressed with gzip and will compress its output. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence ignore lint's version warning). * Update MD5 sum. Actually, 7029066c27ac6f5ef18d660d5741979a is the MD5 sum of an empty file compressed with `gzip --no-name`… This happened because I forgot to update the config file after correcting the module… sorry ! * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change name as suggested in pull request. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 07:59:23 +00:00
last/mafswap:
- software/last/mafswap/**
- tests/software/last/mafswap/**
New module last/postmask to filter alignment files (#526) The `last-postmask` tool distributed with [LAST](https://gitlab.com/mcfrith/last) filters alignments in a MAF file to remove those with too many masked (lower-case) positions compared with their score. As other filter modules like `last/split`, its output file risks to overwrite its input file as their names are constructed from the sample ID when multiple filters are chained in the pipeline. I added a check that gives a clearer error message in this case. Please let me know what you think about; I can add this test to the existing LAST modules as well. This new module is part of the work discribed in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency. We will upgrade it later.
2021-06-08 09:14:08 +00:00
last/postmask:
- software/last/postmask/**
- tests/software/last/postmask/**
New last/split module to find split alignments. (#511) * New last/split module to find split alignments. The `last-split` tool distributed with [LAST](https://gitlab.com/mcfrith/last) finds split or spliced alignments in a MAF file that is produced with, for example, LAST `lastal` command. This new module is part of the work discribed in Issue #464. During this development, we fix the versiob of LAST to 1219 to ensure consistency. We will upgrade it later. * Update software/last/split/main.nf * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-24 19:15:57 +00:00
last/split:
- software/last/split/**
- tests/software/last/split/**
New last/train module to train alignment parameters. (#492) * New last/train module to train alignment parameters. The last-train command creates a parameter file that will be used by last/lastal module for sequence alignment. It takes indexed sequences and query sequences as input and we use the metadata of both to create an id of the parameter output file. Submission of the LAST modules is discussed in more details in the issue #464. For consistancy, we use LAST version 1219 for this whole development and will upgrade later. * Corrected files according to the nf-core v1.14 standards. * Fixed function.nf file for the last-train module. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Find index name. * Correct after the input channels were changed. * Use double underscore as a name separator. Single underscores can happen in ids, therefore, we would like to keep two underscores. * Remove extra spaces. * Fixed the passing of the "score matrix" line. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/last/train/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-19 07:37:08 +00:00
last/train:
- software/last/train/**
- tests/software/last/train/**
🏋️‍♀️ new submodule mash/sketch🕺 (#426) * new submodule mash/sketch * fixed submodule naming * OK, tag is diff to keyword * OK another round :rofl: * removed TODO comments * updated as per review comments :ok_man: * updated functions.nf :grin: * Update software/mash/sketch/main.nf * Update main.nf Removed blank line at the 12th Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-10 15:24:23 +00:00
mash/sketch:
- software/mash/sketch/**
- tests/software/mash/sketch/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
methyldackel/extract:
add methyldackel/extract + tests + testdata
2021-02-17 18:18:55 +00:00
- software/methyldackel/extract/**
- tests/software/methyldackel/extract/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
methyldackel/mbias:
add methyldackel/mbias + tests
2021-02-17 18:27:57 +00:00
- software/methyldackel/mbias/**
- tests/software/methyldackel/mbias/**
Adding minia for viralrecon (#267) * initial 'modules create' of minia * fixed tests * finished meta.yml * fixed filters.yml * resolved issues in pytest_software.yml * add newline * Update software/minia/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 11:54:15 +00:00
minia:
- software/minia/**
- tests/software/minia/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
minimap2/align:
Add minimap2 align module
2021-02-04 19:42:08 +00:00
- software/minimap2/align/**
- tests/software/minimap2/align/**
add minimap2 index module (#467)
2021-04-30 12:18:11 +00:00
minimap2/index:
- software/minimap2/index/**
- tests/software/minimap2/index/**
Adding mosdepth module
2021-02-15 13:33:44 +00:00
mosdepth:
- software/mosdepth/**
- tests/software/mosdepth/**
Added kallistobustools/ref (#408) * Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me * Removed trailing whitespace line 29 * Moved workflow from meta to options. * Update main.nf * Forgot to remove previous testing input channel for workflow. * Apply suggestions from code review Applied changes suggested by @drpatelh Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added gtf to meta.yml. * Apply suggestions from code review Adding @drpatelh suggested changes. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Moved workflow to input value. Fixed tests. * Update tests/software/kallistobustools/ref/test.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 08:41:41 +00:00
msisensor/msi:
Add module: nf-core hackathon #207 : new module: msisensor/msi (#343) * Add module: nf-core hackathon #207 : new module: msisensor/msi * Add module: nf-core hackathon #207 : new module: msisensor/msi * Fix 4-spacing issues (caught in PR linting) * Code review fixes & update configs * Code review: remove stray echo * Code review: Add msisensor modules * Slashes to underscores to get tests to run on github * Update software/msisensor/scan/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/msisensor/scan/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/msisensor/msi/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/msisensor/msi/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Add all outputs to meta.ymls * Fixes from code review * Fixes from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 20:46:00 +00:00
- software/msisensor/msi/**
- tests/software/msisensor/msi/**
Added kallistobustools/ref (#408) * Added kallistobustools/ref. Local tests all passing with Docker. Linting passed. Test data currently in /tests/data/delete_me * Removed trailing whitespace line 29 * Moved workflow from meta to options. * Update main.nf * Forgot to remove previous testing input channel for workflow. * Apply suggestions from code review Applied changes suggested by @drpatelh Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added gtf to meta.yml. * Apply suggestions from code review Adding @drpatelh suggested changes. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Moved workflow to input value. Fixed tests. * Update tests/software/kallistobustools/ref/test.yml * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 08:41:41 +00:00
msisensor/scan:
PR for sequenzautils/bam2seqz (#395) * added files * edited files * removed file * README.md edited Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-04-01 05:08:27 +00:00
- software/msisensor/scan/**
- tests/software/msisensor/scan/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
multiqc:
Fix multiqc tests
2021-02-03 17:43:14 +00:00
- software/fastqc/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/multiqc/**
- tests/software/multiqc/**
add nanolyse module (from nanoseq modules) (#471) * add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-05 10:20:09 +00:00
nanolyse:
- software/nanolyse/**
- tests/software/nanolyse/**
Nanoplot and sequencing_summary.txt for Nanopore test data (#364) * add nanoplot * add Nanopore 100 read subset bam and fastq * add nanoplot module and sequencing_summary.txt * Update pytest_software.yml * Update main.nf * test directory path * testing one output file * Update main.nf * fix typo * remove path to test outputs (it worked locally) * use test_data.config in test * add meta.yml * allowing either summary.txt or fastq.gz inputs * fix linting and test.yml * test whether github check can catch the output * add summary.txt test output paths * check Nanoplot-report.html output
2021-04-09 07:31:38 +00:00
nanoplot:
- software/nanoplot/**
- tests/software/nanoplot/**
Add Nextclade module (#484) * Bump pangolin version * Add nextclade to software list * Add nextclade module * Update md5sum for Pangolin due to version bump * Adding some URL to meta.yml * Adding new line at end of file Co-authored-by: JoseEspinosa <kadomu@gmail.com>
2021-05-06 14:48:15 +00:00
nextclade:
- software/nextclade/**
- tests/software/nextclade/**
Add in OptiType (configbuilder, type) module(s) (#301) * Adding in optitype prototype (To be worked on these days) * I've tried my best :laugh: * No idea * Add in YML stuff * Fix paths * Ok, lets try this * Adding proper options * Replacec configbuilder thing * Fix seq_type * Adding human bam - sarscov doesnt work * Fix a bunch of things * -def * Make this test run * Fancy as fuck * Update tests/software/optitype/test.yml * Add proper tag * Remove md5sums Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-03-23 15:48:05 +00:00
optitype:
- software/optitype/**
- tests/software/optitype/**
Pairtools dedup (#519) * add software/pairtools * create a branch for pairtools/dedup * remove dedup from the filename.
2021-05-27 16:51:27 +00:00
pairtools/dedup:
- software/pairtools/dedup/**
- tests/software/pairtools/dedup/**
add software/pairix (#508) * add software/pairix * Update the functions.nf to new version. Remove -p parameter and fix version output command. fix the duplicated documentation.
2021-05-25 20:22:57 +00:00
New last/dotplot module for pairwise similarity plots (#529) * New last/dotplot module for pairwise similarity plots The `last-dotplot` tool takes a pairwise alignment in [MAF](http://genome.ucsc.edu/FAQ/FAQformat.html#format5) format, possibly compressed with gzip, or in a tabular format produced by the `maf-convert` tool, and produces a similarity dot-plot of the two sequences in one of the graphical formats supported by the Python Imaging Library. A the tool guesses the output format by the file extension of the file, which is constructed by the module at run time, I have used the `args2` option to convey this information to the module. This new module is part of the work described in Issue #464. During this development, we fix the version of LAST to 1219 to ensure consistency (hence please ignore lint's version warning). * Update the functions.nf file to the dev branch. https://raw.githubusercontent.com/nf-core/tools/dev/nf_core/module-template/software/functions.nf
2021-06-08 09:13:51 +00:00
pairtools/flip:
- software/pairtools/flip/**
- tests/software/pairtools/flip/**
Pairtools parse (#521) * add software/pairtools * create a branch for pairtools/parse * fix the issue of bioconda output is different from docker. * remove customized code from test. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-27 17:15:54 +00:00
pairtools/parse:
- software/pairtools/parse/**
- tests/software/pairtools/parse/**
Pairtools sort (#524) * add software/pairtools * create a branch for pairtools/sort * fix the different output of conda and docker. * remove customized code. * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-05-27 17:25:23 +00:00
pairtools/sort:
- software/pairtools/sort/**
- tests/software/pairtools/sort/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
pangolin:
- software/pangolin/**
- tests/software/pangolin/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
picard/collectmultiplemetrics:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/picard/collectmultiplemetrics/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/picard/collectmultiplemetrics/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
picard/collectwgsmetrics:
add picard_collectwgsmetrics (#304) * Added new module picard/collectwgsmetrics. * Removed unused outputs from meta.yml * Added version.txt file back to meta.yml * Updated test.yml * Removed md5sum from test.yaml and added contain tests. * Update functions.nf Fixed missing newline formatting. * Update main.nf Fixed missing newline formatting. * style(picard): Remove trailing whitespace Co-authored-by: Kevin Menden <kevin.menden@t-online.de> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-22 16:05:59 +00:00
- software/picard/collectwgsmetrics/**
- tests/software/picard/collectwgsmetrics/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
picard/markduplicates:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/picard/markduplicates/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/picard/markduplicates/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
picard/mergesamfiles:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/picard/mergesamfiles/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/picard/mergesamfiles/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml
2021-04-08 21:44:30 +00:00
plasmidid:
- software/plasmidid/**
- tests/software/plasmidid/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
preseq/lcextrap:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/preseq/lcextrap/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/preseq/lcextrap/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Prodigal (#333) * WIP add prodigal * Implement module and add tests * Fix EC lint
2021-03-23 18:03:58 +00:00
prodigal:
- software/prodigal/**
- tests/software/prodigal/**
add prokka module (#298) * add prokka module * adjust test outputs * fix prokka command * adjust test outputs * handle optional input * update pytest * update pytest * adjust test outputs * adjust test outputs * switch to lists for optional inputs, add md5sums for non-timestamped outputs * add optional prodigal training file * add optional prodigal training info to meta yaml
2021-03-23 09:51:23 +00:00
prokka:
- software/prokka/**
- tests/software/prokka/**
Add pycoqc module (#424) * Add pycoqc module * Adding pycoqc module tests * Update pycoqc wilth new functions.nf * Update tests to check for json report content
2021-04-12 09:52:14 +00:00
pycoqc:
- software/pycoqc/**
- tests/software/pycoqc/**
add qcat module (from nanoseq modules) (#469) * add qcat module * remove md5sum(nom-reproducible)
2021-04-30 12:20:56 +00:00
qcat:
- software/qcat/**
- tests/software/qcat/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
qualimap/bamqc:
add qualimap/bamqc + test
2021-02-17 16:34:51 +00:00
- software/qualimap/bamqc/**
- tests/software/qualimap/bamqc/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
quast:
- software/quast/**
- tests/software/quast/**
add rapidnj module (#421) * add rapidnj module * remove trailing whitespace * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-09 12:04:54 +00:00
rapidnj:
- software/rapidnj/**
- tests/software/rapidnj/**
🏋️‍♀️ new submodule mash/sketch🕺 (#426) * new submodule mash/sketch * fixed submodule naming * OK, tag is diff to keyword * OK another round :rofl: * removed TODO comments * updated as per review comments :ok_man: * updated functions.nf :grin: * Update software/mash/sketch/main.nf * Update main.nf Removed blank line at the 12th Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-10 15:24:23 +00:00
rasusa:
- software/rasusa/**
- tests/software/rasusa/**
Raxmlng (#443) * new raxml module * new raxml module * pass in args for bootstrap and add test for support file * remove unnecessary tag * ensure tags meet guidleines * Apply suggestions from code review * Update to latest functions file Co-authored-by: avantonder <avt@sanger.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-14 07:38:59 +00:00
raxmlng:
- software/raxmlng/**
- tests/software/raxmlng/**
Finish rseqc modules (#439) * initial 'modules create' of minia * fixed tests * finished meta.yml * fixed filters.yml * resolved issues in pytest_software.yml * add newline * Update software/minia/main.nf * fixing a bunch of module tests * remove vscode * fixed minia * added rseqc/bamstat tests * added tests/meta.yml for rseqc/inferexperiment * added test/meta.yml for rseqc/inner_distances * added meta.yml and tests/main.nf for junctionannotation (test not running) * added test/meta.yml for rseqc/readdistribution * finished test/meta.yml for rseqc/readduplication * added entries to pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-13 07:49:32 +00:00
rseqc/bamstat:
- software/rseqc/bamstat/**
- tests/software/rseqc/bamstat/**
rseqc/inferexperiment:
- software/rseqc/inferexperiment/**
- tests/software/rseqc/inferexperiment/**
rseqc/innerdistance:
- software/rseqc/innerdistance/**
- tests/software/rseqc/innerdistance/**
rseqc/readdistribution:
- software/rseqc/readdistribution/**
- tests/software/rseqc/readdistribution/**
rseqc/readduplication:
- software/rseqc/readduplication/**
- tests/software/rseqc/readduplication/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
salmon/index:
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
- software/salmon/index/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/salmon/index/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
salmon/quant:
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
- software/salmon/quant/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/salmon/quant/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
samtools/faidx:
faidx: add filter
2021-02-17 16:01:22 +00:00
- software/samtools/faidx/**
- tests/software/samtools/faidx/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
samtools/fastq:
new module: samtools/fastq (#316) * new module: samtools/fastq * solve conflict: pytest_software.yml * solve linting conflicts * solved EditorConfig linting problem
2021-03-23 11:13:07 +00:00
- software/samtools/fastq/**
- tests/software/samtools/fastq/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
samtools/flagstat:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/samtools/flagstat/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/samtools/flagstat/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
samtools/idxstats:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/samtools/idxstats/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/samtools/idxstats/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
samtools/index:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/samtools/index/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/samtools/index/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
samtools/merge:
add samtools merge (#296) * add samtools merge * Update pytest_software.yml * get it back to 20.11.0-edge * Update test.yml * Update test.yml * Update test.yml * Update test.yml
2021-03-22 12:48:23 +00:00
- software/samtools/merge/**
- tests/software/samtools/merge/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
samtools/mpileup:
Add in OptiType (configbuilder, type) module(s) (#301) * Adding in optitype prototype (To be worked on these days) * I've tried my best :laugh: * No idea * Add in YML stuff * Fix paths * Ok, lets try this * Adding proper options * Replacec configbuilder thing * Fix seq_type * Adding human bam - sarscov doesnt work * Fix a bunch of things * -def * Make this test run * Fancy as fuck * Update tests/software/optitype/test.yml * Add proper tag * Remove md5sums Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-03-23 15:48:05 +00:00
- software/samtools/mpileup/**
- tests/software/samtools/mpileup/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
samtools/sort:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/samtools/sort/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/samtools/sort/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
samtools/stats:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/samtools/stats/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/samtools/stats/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
samtools/view:
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
- software/samtools/view/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/samtools/view/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
seacr/callpeak:
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
- software/seacr/callpeak/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/seacr/callpeak/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
seqkit/split2:
add seqkit to GHA
2021-02-23 11:43:30 +00:00
- software/seqkit/split2/**
- tests/software/seqkit/split2/**
Update .github/filters.yml Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-02-24 09:29:13 +00:00
Request to review code for seqtk/sample module (#488) * added files * removed file * added file * changed files * changed files * edited file * edited file * edited files * edited files * edited files * edited tags * edited tags * edited tags * edited tags Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-05-09 22:55:35 +00:00
seqtk/sample:
- software/seqtk/sample/**
- tests/software/seqtk/sample/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
sequenzautils/bam2seqz:
PR for sequenzautils/bam2seqz (#395) * added files * edited files * removed file * README.md edited Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
2021-04-01 05:08:27 +00:00
- software/sequenzautils/bam2seqz/**
- tests/software/sequenzautils/bam2seqz/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
sequenzautils/gcwiggle:
PR for sequenzautils/gcwiggle (#345) * added files * edited files * edited files * edited file * test(sequenzautils): Remove md5sum Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com> Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-24 05:03:03 +00:00
- software/sequenzautils/gcwiggle/**
- tests/software/sequenzautils/gcwiggle/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
seqwish/induce:
Add module for seqwish/induce
2021-02-17 17:19:47 +00:00
- software/seqwish/induce/**
- tests/software/seqwish/induce/**
add seqkit to GHA
2021-02-23 11:43:30 +00:00
Update shovill module (#337) * add shovill module * removed deprecated shovill module * fix line ending in functions.nf * fix yaml indentation * reduce spades memory usage * update md5sums * remove non reproducible md5sum * Update test.yml Remove last non-reproducible md5sum. * purely cosmetic order change * proper process label, improve output readability Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
2021-03-24 04:57:41 +00:00
shovill:
- software/shovill/**
- tests/software/shovill/**
New Snpsites module (#416) * new gubbins module * new gubbins module * new gubbins module * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/gubbins/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * new gubbins module * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/gubbins/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * new gubbins module * new gubbins module * new snpsites module * new snpsites module * new snpsites module * new snpsites module * adding fasttree module * correct trailing whitespace * using sarscov2 as a test dir * use sars-cov-2 alignment * remove old test alignment * new snpsites module * new snpsites module * new snpsites module * updated test file names * new snpsites module * revert to gubbins test on upstream * add new lines * renove whitespace * Apply suggestions from code review Co-authored-by: avantonder <avt@sanger.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: avantonder <ajv37@cam.ac.uk>
2021-04-09 07:00:33 +00:00
snpsites:
- software/snpsites/**
- tests/software/snpsites/**
Add spades module (#277) * Add spades module * Reorder gatk4 modules alphabetically * Update software/spades/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-18 13:48:38 +00:00
spades:
- software/spades/**
- tests/software/spades/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
star/align:
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
- software/star/align/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/star/align/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
star/genomegenerate:
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
- software/star/genomegenerate/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/star/genomegenerate/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
strelka/germline:
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
2021-03-24 05:07:29 +00:00
- software/strelka/germline/**
- tests/software/strelka/germline/**
Add stringtie merge module (from nanoseq modules) (#475) * add stringtie merge module * add md5sum and path for stringtie.merged.gtf * fix errors * try fixing stringtie check error * add tag * remove unreproducible md5sum * address PR suggestions * hopefully fix linting error
2021-05-03 05:18:51 +00:00
stringtie/merge:
- software/stringtie/merge/**
- tests/software/stringtie/merge/**
stringtie/stringtie:
- software/stringtie/stringtie/**
- tests/software/stringtie/stringtie/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
subread/featurecounts:
Add tests for subread #106 (#393) * inital commit * added meta.yaml info * add initial logic for featurecounts test * add args and change SE/PE to strandedness for featurecounts test * added tests to pytest * added test.yml * removed GTF flag in options * corrected test meta params * meta yaml corrected tool info * update test.yml * fix lint errors meta.yml Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
2021-04-01 19:02:36 +00:00
- software/subread/featurecounts/**
- tests/software/subread/featurecounts/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
tabix/bgzip:
chores: replace bcftools/bgzip by tabix/bgzip cf #179
2021-02-16 18:11:36 +00:00
- software/tabix/bgzip/**
- tests/software/tabix/bgzip/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
tabix/tabix:
fix: order alphabetically
2021-02-19 09:56:04 +00:00
- software/tabix/tabix/**
- tests/software/tabix/tabix/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
tiddit/sv:
feat: add tiddit_sv module
2021-02-24 14:59:10 +00:00
- software/tiddit/sv/**
- tests/software/tiddit/sv/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
trimgalore:
- software/trimgalore/**
- tests/software/trimgalore/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
ucsc/bed12tobigbed:
ucsc_bed12tobigbed (previous pull request had conflicts) (#302) * Add files via upload * Add files via upload * Add files via upload * Add files via upload * Update pytest_software.yml * Update main.nf * fix linting error * Delete test.yml * Create functions.nf * Update main.nf * change test data * revert to !>=20.11.0-edge
2021-03-24 04:55:49 +00:00
- software/ucsc/bed12tobigbed/**
- tests/software/ucsc/bed12tobigbed/**
Add ucsc/bedclip module (#450) * Add ucsc/bedclip module * Fix tests * Fix nf-core lint
2021-04-15 20:04:59 +00:00
ucsc/bedclip:
- software/ucsc/bedclip/**
- tests/software/ucsc/bedclip/**
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
ucsc/bedgraphtobigwig:
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
- software/ucsc/bedgraphtobigwig/**
Fix barfing linters
2021-02-08 00:57:06 +00:00
- tests/software/ucsc/bedgraphtobigwig/**
added gatk4 variantfiltration (#265) * added gatk4 variantfiltration * replace merge with filter * Update software/gatk4/variantfiltration/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * updated input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 08:42:35 +00:00
add additional ucsc tools (#506) * add additional ucsc tools * Update software/ucsc/wigtobigwig/meta.yml Co-authored-by: Kevin Menden <kevin.menden@live.com> * Update the functions.nf and software name for ucsc/wigtobigwig and bigwigaverageoverbed. Co-authored-by: Kevin Menden <kevin.menden@live.com>
2021-05-20 19:39:33 +00:00
ucsc/bigwigaverageoverbed:
- software/ucsc/bigwigaverageoverbed/**
- tests/software/ucsc/bigwigaverageoverbed/**
ucsc/wigtobigwig:
- software/ucsc/wigtobigwig/**
- tests/software/ucsc/wigtobigwig/**
Adding unicycler module (#307) * Adding unicycler module * Do not forget to change default keywords on meta.yml
2021-03-22 17:14:24 +00:00
unicycler:
- software/unicycler/**
- tests/software/unicycler/**
Adding minia for viralrecon (#267) * initial 'modules create' of minia * fixed tests * finished meta.yml * fixed filters.yml * resolved issues in pytest_software.yml * add newline * Update software/minia/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-17 11:54:15 +00:00
untar:
- software/untar/**
- tests/software/untar/**
add vcftools module (#334) * add vcftools module * fix padding issue * fix linting errors
2021-03-24 04:54:23 +00:00
vcftools:
- software/vcftools/**
- tests/software/vcftools/**
Add YARA module (#353) * Initial work on yara module * Adding in index basics * Updated the index stuff * Adding in proper tests * Fix editorconfig * Odd paths * that should do it * Fix tests * Fix tests * FFS * Once more * Mapping is not deterministic
2021-03-24 16:14:52 +00:00
Lint modules ci (#389) * ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-08 08:10:52 +00:00
yara/index:
Add YARA module (#353) * Initial work on yara module * Adding in index basics * Updated the index stuff * Adding in proper tests * Fix editorconfig * Odd paths * that should do it * Fix tests * Fix tests * FFS * Once more * Mapping is not deterministic
2021-03-24 16:14:52 +00:00
- software/yara/index/**
- tests/software/yara/index/**
Add abacas module (#431) * Add abacas module * Add test for abacas module * Add Harshil to authorship * Updating test with the data uploaded to nf-core/datasets * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-04-12 14:37:08 +00:00
yara/mapper:
- software/yara/mapper/**
- tests/software/yara/mapper/**
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