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nf-core_modules/tests/config/pytest_software.yml

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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/**
Address review comments
2021-02-04 18:10:54 +00:00
bandage_image:
- software/bandage/image/**
- tests/software/bandage/image/**
Adding again bcftools modules to filters after solving conflict
2021-02-08 17:10:50 +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
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
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
Add bcftools merge module
2021-02-12 23:08:57 +00:00
bcftools_merge:
- software/bcftools/merge/**
- tests/software/bcftools/merge/**
Add tests for bcftools-mpileup
2021-02-23 18:05:57 +00:00
bcftools_mpileup:
- software/bcftools/mpileup/**
- tests/software/bcftools/mpileup/**
Adding again bcftools modules to filters after solving conflict
2021-02-08 17:10:50 +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
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
bedtools_complement:
- software/bedtools/complement/**
- tests/software/bedtools/complement/**
bedtools_genomecov:
- software/bedtools/genomecov/**
- tests/software/bedtools/genomecov/**
Add bedtools getfasta module
2021-02-09 16:56:51 +00:00
bedtools_getfasta:
- software/bedtools/getfasta/**
- tests/software/bedtools/getfasta/**
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
bedtools_intersect:
- software/bedtools/intersect/**
- tests/software/bedtools/intersect/**
Add bedtools maskfasta module
2021-02-08 22:41:10 +00:00
bedtools_maskfasta:
- software/bedtools/maskfasta/**
- tests/software/bedtools/maskfasta/**
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
bedtools_merge:
- software/bedtools/merge/**
- tests/software/bedtools/merge/**
bedtools_slop:
- software/bedtools/slop/**
- tests/software/bedtools/slop/**
bedtools_sort:
- software/bedtools/sort/**
- tests/software/bedtools/sort/**
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
bismark_align:
- 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/**
add bismark/deduplicate + tests
2021-02-23 17:02:16 +00:00
bismark_deduplicate:
- software/bismark/deduplicate/**
- tests/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
bismark_genomepreparation:
- software/bismark/genomepreparation/**
- tests/software/bismark/genomepreparation/**
add bismark/genome_preparation + tests
2021-02-18 09:56:36 +00:00
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
bismark_methylationextractor:
- 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
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
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/**
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
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/**
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
blast_blastn:
- 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
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
blast_makeblastdb:
- software/blast/makeblastdb/**
- tests/software/blast/makeblastdb/**
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
bowtie2_align:
- software/bowtie2/align/**
- software/bowtie2/build/**
- tests/software/bowtie2/align/**
Adding blast makeblastdb module to filters.yml
2021-02-09 14:47:53 +00:00
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
bowtie2_build:
- software/bowtie2/build/**
- tests/software/bowtie2/build_test/**
Rename SOFTWARE_TOOL to TOOL_SUBTOOL
2021-02-07 23:20:53 +00:00
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
bowtie_align:
- 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
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
bowtie_build:
- software/bowtie/build/**
- tests/software/bowtie/build_test/**
Update filters paths
2021-02-03 16:04:43 +00:00
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
bwa_index:
- 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
bwa_mem:
- 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
chores: update filters.yml
2021-02-12 12:53:49 +00:00
bwamem2_index:
- software/bwamem2/index/**
- tests/software/bwamem2/index/**
bwamem2_mem:
- software/bwamem2/mem/**
- tests/software/bwamem2/mem/**
add bwameth/align module + tests
2021-02-17 17:23:11 +00:00
bwameth_align:
- software/bwameth/align/**
- tests/software/bwameth/align/**
add bwameth/index module + test
2021-02-17 17:03:48 +00:00
bwameth_index:
- software/bwameth/index/**
- tests/software/bwameth/index/**
Add cat fastq module
2021-02-12 16:22:07 +00:00
cat_fastq:
- 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/**
dsh_filterbed:
- software/dsh/filterbed/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/dsh/filterbed/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
dsh_splitbed:
- software/dsh/splitbed/**
Update filters paths
2021-02-03 16:04:43 +00:00
- tests/software/dsh/splitbed/**
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
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/**
Add gatk4/applybqsr (#331) * Add applybqsr module * Solve problem in functions.nf * Add to pytest
2021-03-23 13:15:26 +00:00
gatk4_applybqsr:
- software/gatk4/applybqsr/**
- tests/software/gatk4/applybqsr/**
Add gatk4/baserecalibrator (#327) * Add gatk4 BaseRecalibrator * Solve format in main.nf * Correct functions * Add pytest
2021-03-23 17:32:37 +00:00
gatk4_baserecalibrator:
- software/gatk4/baserecalibrator/**
- tests/software/gatk4/baserecalibrator/**
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
gatk4_bedtointervallist:
- software/gatk4/bedtointervallist/**
- tests/software/gatk4/bedtointervallist/**
gatk4_createsequencedictionary:
- software/gatk4/createsequencedictionary/**
- tests/software/gatk4/createsequencedictionary/**
chores: add gatk/createsequencedictionary module
2021-02-16 12:40:06 +00:00
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
gatk4_fastqtosam:
- software/gatk4/fastqtosam/**
- tests/software/gatk4/fastqtosam/**
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
gatk4_haplotypecaller:
- software/gatk4/haplotypecaller/**
- tests/software/gatk4/haplotypecaller/**
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
gatk4_mergebamalignment:
- software/gatk4/mergebamalignment/**
- tests/software/gatk4/mergebamalignment/**
working test
2021-02-19 12:36:42 +00:00
gatk4_mergevcfs:
- software/gatk4/mergevcfs/**
- tests/software/gatk4/mergevcfs/**
added gatk4 revertsam
2021-02-22 14:21:39 +00:00
gatk4_revertsam:
- software/gatk4/revertsam/**
- tests/software/gatk4/revertsam/**
added gatk4 SamToFastq
2021-02-19 11:41:29 +00:00
gatk4_samtofastq:
- software/gatk4/samtofastq/**
- tests/software/gatk4/samtofastq/**
add gatk4 bedtointervallist
2021-02-19 10:26:31 +00:00
added entry to filters.yml
2021-02-22 12:36:49 +00:00
gatk4_splitncigarreads:
- software/gatk4/splitncigarreads/**
- tests/software/gatk4/splitncigarreads/**
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
gatk4_variantfiltration:
- software/gatk4/variantfiltration/**
- tests/software/gatk4/variantfiltration/**
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 gunzip module
2021-02-09 09:05:55 +00:00
gunzip:
- software/gunzip/**
- tests/software/gunzip/**
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
hisat2_align:
- software/hisat2/align/**
- software/hisat2/build/**
- software/hisat2/extractsplicesites/**
- tests/software/hisat2/align/**
hisat2_build:
- software/hisat2/build/**
- software/hisat2/extractsplicesites/**
- tests/software/hisat2/build_test/**
hisat2_extractsplicesites:
- software/hisat2/extractsplicesites/**
- tests/software/hisat2/extractsplicesites/**
Homer (#330) * started with homer * added tests for homer annotatepeaks * fix md5 * remove md5 sum
2021-03-23 18:24:54 +00:00
homer_annotatepeaks:
- software/homer/annotatepeaks/**
- tests/software/homer/annotatepeaks/**
Add ivar consensus to filter.yml
2021-02-12 18:59:46 +00:00
ivar_consensus:
- software/ivar/consensus/**
- tests/software/ivar/consensus/**
Add ivar trim
2021-02-13 00:02:10 +00:00
ivar_trim:
- software/ivar/trim/**
- tests/software/ivar/trim/**
Add ivar variants
2021-02-15 17:28:10 +00:00
ivar_variants:
- software/ivar/variants/**
- tests/software/ivar/variants/**
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
kallisto_index:
- software/kallisto/index/**
- tests/software/kallisto/index/**
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
kraken2_run:
- software/kraken2/run/**
- tests/software/kraken2/run/**
add methyldackel/extract + tests + testdata
2021-02-17 18:18:55 +00:00
methyldackel_extract:
- software/methyldackel/extract/**
- tests/software/methyldackel/extract/**
add methyldackel/mbias + tests
2021-02-17 18:27:57 +00:00
methyldackel_mbias:
- 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/**
Add minimap2 align module
2021-02-04 19:42:08 +00:00
minimap2_align:
- software/minimap2/align/**
- tests/software/minimap2/align/**
Adding mosdepth module
2021-02-15 13:33:44 +00:00
mosdepth:
- software/mosdepth/**
- tests/software/mosdepth/**
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
msisensor_scan:
- software/msisensor/scan/**
- tests/software/msisensor/scan/**
msisensor_msi:
- software/msisensor/msi/**
- tests/software/msisensor/msi/**
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 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/**
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/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
picard_collectmultiplemetrics:
- 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
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
picard_collectwgsmetrics:
- software/picard/collectwgsmetrics/**
- tests/software/picard/collectwgsmetrics/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
picard_markduplicates:
- 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
picard_mergesamfiles:
- 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
preseq_lcextrap:
- 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 qualimap/bamqc + test
2021-02-17 16:34:51 +00:00
qualimap_bamqc:
- 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/**
salmon_index:
- 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
salmon_quant:
- 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
faidx: add filter
2021-02-17 16:01:22 +00:00
samtools_faidx:
- software/samtools/faidx/**
- tests/software/samtools/faidx/**
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
samtools_fastq:
- software/samtools/fastq/**
- tests/software/samtools/fastq/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
samtools_flagstat:
- 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
samtools_idxstats:
- 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
samtools_index:
- 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
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
samtools_merge:
- software/samtools/merge/**
- tests/software/samtools/merge/**
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
samtools_mpileup:
- software/samtools/mpileup/**
- tests/software/samtools/mpileup/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
samtools_sort:
- 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
samtools_stats:
- 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
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
samtools_view:
- 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
seacr_callpeak:
- 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
add seqkit to GHA
2021-02-23 11:43:30 +00:00
seqkit_split2:
- 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
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
sequenza_bam2seqz:
- software/sequenza/bam2seqz/**
- tests/software/sequenza/bam2seqz/**
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
sequenza_wiggle:
- software/sequenza/wiggle/**
- tests/software/sequenza/wiggle/**
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
sequenzautils_gcwiggle:
- software/sequenzautils/gcwiggle/**
- tests/software/sequenzautils/gcwiggle/**
Add module for seqwish/induce
2021-02-17 17:19:47 +00:00
seqwish_induce:
- 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/**
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/**
ci: Add filters for new modules These snuck in after the 506ebe5 was written
2021-02-02 21:27:45 +00:00
star_align:
- 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
star_genomegenerate:
- 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
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
strelka_germline:
- software/strelka/germline/**
- tests/software/strelka/germline/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
stringtie:
Update filters paths
2021-02-03 16:04:43 +00:00
- software/stringtie/**
- tests/software/stringtie/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
chores: replace bcftools/bgzip by tabix/bgzip cf #179
2021-02-16 18:11:36 +00:00
tabix_bgzip:
- software/tabix/bgzip/**
- tests/software/tabix/bgzip/**
fix: order alphabetically
2021-02-19 09:56:04 +00:00
tabix_tabix:
- software/tabix/tabix/**
- tests/software/tabix/tabix/**
feat: add tiddit_sv module
2021-02-24 14:59:10 +00:00
tiddit_sv:
- 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/**
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
ucsc_bed12tobigbed:
- software/ucsc/bed12tobigbed/**
- tests/software/ucsc/bed12tobigbed/**
ci: Move all files to filter file and delete old tests
2021-01-24 05:50:20 +00:00
ucsc_bedgraphtobigwig:
- 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
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
yara:
- software/yara/mapper/**
- tests/software/yara/mapper/**
yara_index:
- software/yara/index/**
- tests/software/yara/index/**
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