nf-core_modules/tests/config/pytest_software.yml

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abacas:
- software/abacas/**
- tests/software/abacas/**
adapterremoval:
- software/adapterremoval/**
- tests/software/adapterremoval/**
allelecounter:
- software/allelecounter/**
- tests/software/allelecounter/**
artic/guppyplex:
- software/artic/guppyplex/**
- tests/software/artic/guppyplex/**
artic/minion:
- software/artic/minion/**
- tests/software/artic/minion/**
bandage/image:
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- software/bandage/image/**
- tests/software/bandage/image/**
bbmap/bbduk:
- software/bbmap/bbduk/**
- tests/software/bbmap/bbduk/**
bcftools/consensus:
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- software/bcftools/consensus/**
- tests/software/bcftools/consensus/**
bcftools/filter:
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- software/bcftools/filter/**
- tests/software/bcftools/filter/**
bcftools/isec:
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- software/bcftools/isec/**
- tests/software/bcftools/isec/**
bcftools/merge:
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- software/bcftools/merge/**
- tests/software/bcftools/merge/**
bcftools/mpileup:
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- software/bcftools/mpileup/**
- tests/software/bcftools/mpileup/**
bcftools/stats:
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- software/bcftools/stats/**
- tests/software/bcftools/stats/**
bedtools/bamtobed:
- software/bedtools/bamtobed/**
- tests/software/bedtools/bamtobed/**
bedtools/complement:
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- software/bedtools/complement/**
- tests/software/bedtools/complement/**
bedtools/genomecov:
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- software/bedtools/genomecov/**
- tests/software/bedtools/genomecov/**
bedtools/getfasta:
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- software/bedtools/getfasta/**
- tests/software/bedtools/getfasta/**
bedtools/intersect:
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- software/bedtools/intersect/**
- tests/software/bedtools/intersect/**
bedtools/maskfasta:
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- software/bedtools/maskfasta/**
- tests/software/bedtools/maskfasta/**
bedtools/merge:
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- software/bedtools/merge/**
- tests/software/bedtools/merge/**
bedtools/slop:
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- software/bedtools/slop/**
- tests/software/bedtools/slop/**
bedtools/sort:
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- software/bedtools/sort/**
- tests/software/bedtools/sort/**
bismark/align:
- software/bismark/align/**
- software/bismark/genomepreparation/**
- tests/software/bismark/align/**
bismark/deduplicate:
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- software/bismark/deduplicate/**
- tests/software/bismark/deduplicate/**
bismark/genomepreparation:
- software/bismark/genomepreparation/**
- tests/software/bismark/genomepreparation/**
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bismark/methylationextractor:
- software/bismark/methylationextractor/**
- software/bismark/genomepreparation/**
- tests/software/bismark/methylationextractor/**
bismark/report:
- software/bismark/genomepreparation/**
- software/bismark/align/**
- software/bismark/deduplicate/**
- software/bismark/methylationextractor/**
- software/bismark/report/**
- tests/software/bismark/report/**
bismark/summary:
- software/bismark/genomepreparation/**
- software/bismark/align/**
- software/bismark/deduplicate/**
- software/bismark/methylationextractor/**
- software/bismark/summary/**
- tests/software/bismark/summary/**
blast/blastn:
- software/blast/blastn/**
- tests/software/blast/blastn/**
blast/makeblastdb:
- software/blast/makeblastdb/**
- tests/software/blast/makeblastdb/**
bowtie/align:
- software/bowtie/align/**
- software/bowtie/build/**
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- tests/software/bowtie/align/**
bowtie/build:
- software/bowtie/build/**
- tests/software/bowtie/build_test/**
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bowtie2/align:
- software/bowtie2/align/**
- software/bowtie2/build/**
- tests/software/bowtie2/align/**
bowtie2/build:
- software/bowtie2/build/**
- tests/software/bowtie2/build_test/**
bwa/index:
- software/bwa/index/**
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- tests/software/bwa/index/**
bwa/mem:
- software/bwa/mem/**
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- tests/software/bwa/mem/**
bwamem2/index:
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- software/bwamem2/index/**
- tests/software/bwamem2/index/**
bwamem2/mem:
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- software/bwamem2/mem/**
- tests/software/bwamem2/mem/**
bwameth/align:
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- software/bwameth/align/**
- tests/software/bwameth/align/**
bwameth/index:
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- software/bwameth/index/**
- tests/software/bwameth/index/**
cat/fastq:
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- 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/**
cooler/digest:
- software/cooler/digest/**
- tests/software/cooler/digest/**
cooler/dump:
- software/cooler/dump/**
- tests/software/cooler/dump/**
cutadapt:
- software/cutadapt/**
- tests/software/cutadapt/**
damageprofiler:
- software/damageprofiler/**
- tests/software/damageprofiler/**
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/**
dshbio/filterbed:
- software/dshbio/filterbed/**
- tests/software/dshbio/filterbed/**
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/**
fastp:
- software/fastp/**
- tests/software/fastp/**
fastqc:
- software/fastqc/**
- tests/software/fastqc/**
fasttree:
- software/fasttree/**
- tests/software/fasttree/**
fgbio/callmolecularconsensusreads:
- software/fgbio/callmolecularconsensusreads/**
- tests/software/fgbio/callmolecularconsensusreads/**
fgbio/sortbam:
- software/fgbio/sortbam/**
- tests/software/fgbio/sortbam/**
flash:
- software/flash/**
- tests/software/flash/**
gatk4/applybqsr:
- software/gatk4/applybqsr/**
- tests/software/gatk4/applybqsr/**
gatk4/baserecalibrator:
- software/gatk4/baserecalibrator/**
- tests/software/gatk4/baserecalibrator/**
gatk4/bedtointervallist:
- software/gatk4/bedtointervallist/**
- tests/software/gatk4/bedtointervallist/**
gatk4/createsequencedictionary:
- software/gatk4/createsequencedictionary/**
- tests/software/gatk4/createsequencedictionary/**
gatk4/fastqtosam:
- software/gatk4/fastqtosam/**
- tests/software/gatk4/fastqtosam/**
gatk4/haplotypecaller:
- software/gatk4/haplotypecaller/**
- tests/software/gatk4/haplotypecaller/**
gatk4/intervallisttools:
- software/gatk4/intervallisttools/**
- tests/software/gatk4/intervallisttools/**
gatk4/markduplicates:
- software/gatk4/markduplicates/**
- tests/software/gatk4/markduplicates/**
gatk4/mergebamalignment:
- software/gatk4/mergebamalignment/**
- tests/software/gatk4/mergebamalignment/**
gatk4/mergevcfs:
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- software/gatk4/mergevcfs/**
- tests/software/gatk4/mergevcfs/**
gatk4/revertsam:
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- software/gatk4/revertsam/**
- tests/software/gatk4/revertsam/**
gatk4/samtofastq:
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- software/gatk4/samtofastq/**
- tests/software/gatk4/samtofastq/**
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gatk4/splitncigarreads:
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- software/gatk4/splitncigarreads/**
- tests/software/gatk4/splitncigarreads/**
gatk4/variantfiltration:
- software/gatk4/variantfiltration/**
- tests/software/gatk4/variantfiltration/**
genmap/index:
- software/genmap/index/**
- tests/software/genmap/index/**
genmap/mappability:
- software/genmap/mappability/**
- tests/software/genmap/mappability/**
gffread:
- software/gffread/**
- tests/software/gffread/**
graphmap2/align:
- software/graphmap2/align/**
- tests/software/graphmap2/align/**
graphmap2/index:
- software/graphmap2/index/**
- tests/software/graphmap2/index/**
gubbins:
- software/gubbins/**
- tests/software/gubbins/**
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gunzip:
- software/gunzip/**
- tests/software/gunzip/**
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>
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- software/hisat2/align/**
- software/hisat2/build/**
- software/hisat2/extractsplicesites/**
- tests/software/hisat2/align/**
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/**
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/**
hmmer/hmmalign:
- software/hmmer/hmmalign/**
- tests/software/hmmer/hmmalign/**
homer/annotatepeaks:
- software/homer/annotatepeaks/**
- tests/software/homer/annotatepeaks/**
iqtree:
- software/iqtree/**
- tests/software/iqtree/**
ivar/consensus:
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- software/ivar/consensus/**
- tests/software/ivar/consensus/**
ivar/trim:
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- software/ivar/trim/**
- tests/software/ivar/trim/**
ivar/variants:
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- software/ivar/variants/**
- tests/software/ivar/variants/**
kallisto/index:
- software/kallisto/index/**
- tests/software/kallisto/index/**
kallistobustools/count:
- software/kallistobustools/count/**
- tests/software/kallistobustools/count/**
kallistobustools/ref:
- software/kallistobustools/ref/**
- tests/software/kallistobustools/ref/**
kraken2/kraken2:
- software/kraken2/kraken2/**
- software/untar/**
- tests/software/kraken2/kraken2/**
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/**
last/lastdb:
- software/last/lastdb/**
- tests/software/last/lastdb/**
last/mafconvert:
- software/last/mafconvert/**
- tests/software/last/mafconvert/**
last/mafswap:
- software/last/mafswap/**
- tests/software/last/mafswap/**
last/postmask:
- software/last/postmask/**
- tests/software/last/postmask/**
last/split:
- software/last/split/**
- tests/software/last/split/**
last/train:
- software/last/train/**
- tests/software/last/train/**
lofreq/filter:
- software/lofreq/filter/**
- tests/software/lofreq/filter/**
lofreq/indelqual:
- software/lofreq/indelqual/**
- tests/software/lofreq/indelqual/**
mash/sketch:
- software/mash/sketch/**
- tests/software/mash/sketch/**
metaphlan3:
- software/metaphlan3/**
- tests/software/metaphlan3/**
methyldackel/extract:
- software/methyldackel/extract/**
- tests/software/methyldackel/extract/**
methyldackel/mbias:
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- software/methyldackel/mbias/**
- tests/software/methyldackel/mbias/**
minia:
- software/minia/**
- tests/software/minia/**
minimap2/align:
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- software/minimap2/align/**
- tests/software/minimap2/align/**
2021-04-30 12:18:11 +00:00
minimap2/index:
- software/minimap2/index/**
- tests/software/minimap2/index/**
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mosdepth:
- software/mosdepth/**
- tests/software/mosdepth/**
msisensor/msi:
- software/msisensor/msi/**
- tests/software/msisensor/msi/**
msisensor/scan:
- software/msisensor/scan/**
- tests/software/msisensor/scan/**
multiqc:
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- software/fastqc/**
- software/multiqc/**
- tests/software/multiqc/**
2021-06-28 06:20:02 +00:00
muscle:
- software/muscle/**
- tests/software/muscle/**
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:
- software/nanoplot/**
- tests/software/nanoplot/**
nextclade:
- software/nextclade/**
- tests/software/nextclade/**
optitype:
- software/optitype/**
- tests/software/optitype/**
pairix:
- software/pairix/**
- tests/software/pairix/**
pairtools/dedup:
- software/pairtools/dedup/**
- tests/software/pairtools/dedup/**
pairtools/flip:
- software/pairtools/flip/**
- tests/software/pairtools/flip/**
pairtools/parse:
- software/pairtools/parse/**
- tests/software/pairtools/parse/**
pairtools/restrict:
- software/pairtools/restrict/**
- tests/software/pairtools/restrict/**
pairtools/select:
- software/pairtools/select/**
- tests/software/pairtools/select/**
pairtools/sort:
- software/pairtools/sort/**
- tests/software/pairtools/sort/**
pangolin:
- software/pangolin/**
- tests/software/pangolin/**
picard/collectmultiplemetrics:
- software/picard/collectmultiplemetrics/**
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- tests/software/picard/collectmultiplemetrics/**
picard/collectwgsmetrics:
- software/picard/collectwgsmetrics/**
- tests/software/picard/collectwgsmetrics/**
picard/markduplicates:
- software/picard/markduplicates/**
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- tests/software/picard/markduplicates/**
picard/mergesamfiles:
- software/picard/mergesamfiles/**
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- tests/software/picard/mergesamfiles/**
plasmidid:
- software/plasmidid/**
- tests/software/plasmidid/**
preseq/lcextrap:
- software/preseq/lcextrap/**
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- tests/software/preseq/lcextrap/**
prodigal:
- software/prodigal/**
- tests/software/prodigal/**
prokka:
- software/prokka/**
- tests/software/prokka/**
pycoqc:
- software/pycoqc/**
- tests/software/pycoqc/**
qcat:
- software/qcat/**
- tests/software/qcat/**
qualimap/bamqc:
2021-02-17 16:34:51 +00:00
- software/qualimap/bamqc/**
- tests/software/qualimap/bamqc/**
quast:
- software/quast/**
- tests/software/quast/**
rapidnj:
- software/rapidnj/**
- tests/software/rapidnj/**
rasusa:
- software/rasusa/**
- tests/software/rasusa/**
raxmlng:
- software/raxmlng/**
- tests/software/raxmlng/**
rsem/calculateexpression:
- software/rsem/calculateexpression/**
- tests/software/rsem/calculateexpression/**
rsem/preparereference:
- software/rsem/preparereference/**
- tests/software/rsem/preparereference/**
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/junctionannotation:
- software/rseqc/junctionannotation/**
- tests/software/rseqc/junctionannotation/**
rseqc/junctionsaturation:
- software/rseqc/junctionsaturation/**
- tests/software/rseqc/junctionsaturation/**
rseqc/readdistribution:
- software/rseqc/readdistribution/**
- tests/software/rseqc/readdistribution/**
rseqc/readduplication:
- software/rseqc/readduplication/**
- tests/software/rseqc/readduplication/**
salmon/index:
- software/salmon/index/**
2021-02-03 16:04:43 +00:00
- tests/software/salmon/index/**
salmon/quant:
- software/salmon/quant/**
2021-02-03 16:04:43 +00:00
- tests/software/salmon/quant/**
samtools/faidx:
2021-02-17 16:01:22 +00:00
- software/samtools/faidx/**
- tests/software/samtools/faidx/**
samtools/fastq:
- software/samtools/fastq/**
- tests/software/samtools/fastq/**
samtools/flagstat:
- software/samtools/flagstat/**
2021-02-03 16:04:43 +00:00
- tests/software/samtools/flagstat/**
samtools/idxstats:
- software/samtools/idxstats/**
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- tests/software/samtools/idxstats/**
samtools/index:
- software/samtools/index/**
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- tests/software/samtools/index/**
samtools/merge:
- software/samtools/merge/**
- tests/software/samtools/merge/**
samtools/mpileup:
- software/samtools/mpileup/**
- tests/software/samtools/mpileup/**
samtools/sort:
- software/samtools/sort/**
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- tests/software/samtools/sort/**
samtools/stats:
- software/samtools/stats/**
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- tests/software/samtools/stats/**
samtools/view:
- software/samtools/view/**
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- tests/software/samtools/view/**
seacr/callpeak:
- software/seacr/callpeak/**
2021-02-03 16:04:43 +00:00
- tests/software/seacr/callpeak/**
seqkit/split2:
2021-02-23 11:43:30 +00:00
- software/seqkit/split2/**
- tests/software/seqkit/split2/**
seqtk/sample:
- software/seqtk/sample/**
- tests/software/seqtk/sample/**
Feat seqtk update (#503) * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added seqtk/subseq and checking for seed in seqtk/sample * Separate authors in software/seqtk/sample/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Align commans in output channesl software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define prefix in software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Use prefix in output file name software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define suffix in options in tests/software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change output file name in tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove a to-do point from tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added --no-name into gzip commands * Update samtools from 1.10 to 1.12 (#530) * feat: remove social preview image to use GitHub OpenGraph * feat: update samtools from 1.10 to 1.12 * fix: CI tests * fix: add meta.yml file for samtools/merge * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Update software/samtools/merge/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Added seqtk/subseq and checking for seed in seqtk/sample * hifiasm copied from fastqc * hifiasm tests init from fastqc * meta.yml init; test.yml and main.nf for printing version * Add hifiasm version printing * Removed spaced on an empty line * Reverted hifiasm from main * Separate authors in software/seqtk/sample/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Align commans in output channesl software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define prefix in software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Use prefix in output file name software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Define suffix in options in tests/software/seqtk/subseq/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Change output file name in tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Remove a to-do point from tests/software/seqtk/subseq/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Added --no-name into gzip commands * Replaced functions.nf in seqtk/subseq * Refreshed tests for sample and subseq * Corrected paired-end test and YAML description for sample Co-authored-by: Sviatoslav Sidorov <sviatoslav.sidorov@crick.ac.uk> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2021-06-14 11:23:15 +00:00
seqtk/subseq:
- software/seqtk/subseq/**
- tests/software/seqtk/subseq/**
sequenzautils/bam2seqz:
- software/sequenzautils/bam2seqz/**
- tests/software/sequenzautils/bam2seqz/**
sequenzautils/gcwiggle:
- software/sequenzautils/gcwiggle/**
- tests/software/sequenzautils/gcwiggle/**
seqwish/induce:
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- software/seqwish/induce/**
- tests/software/seqwish/induce/**
2021-02-23 11:43:30 +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/**
spades:
- software/spades/**
- tests/software/spades/**
star/align:
- software/star/align/**
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- tests/software/star/align/**
star/genomegenerate:
- software/star/genomegenerate/**
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- tests/software/star/genomegenerate/**
strelka/germline:
- software/strelka/germline/**
- tests/software/strelka/germline/**
stringtie/merge:
- software/stringtie/merge/**
- tests/software/stringtie/merge/**
stringtie/stringtie:
- software/stringtie/stringtie/**
- tests/software/stringtie/stringtie/**
subread/featurecounts:
- software/subread/featurecounts/**
- tests/software/subread/featurecounts/**
tabix/bgzip:
- software/tabix/bgzip/**
- tests/software/tabix/bgzip/**
tabix/bgziptabix:
- software/tabix/bgziptabix/**
- tests/software/tabix/bgziptabix/**
tabix/tabix:
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- software/tabix/tabix/**
- tests/software/tabix/tabix/**
tiddit/sv:
2021-02-24 14:59:10 +00:00
- software/tiddit/sv/**
- tests/software/tiddit/sv/**
trimgalore:
- software/trimgalore/**
- tests/software/trimgalore/**
ucsc/bed12tobigbed:
- software/ucsc/bed12tobigbed/**
- tests/software/ucsc/bed12tobigbed/**
ucsc/bedclip:
- software/ucsc/bedclip/**
- tests/software/ucsc/bedclip/**
ucsc/bedgraphtobigwig:
- software/ucsc/bedgraphtobigwig/**
2021-02-08 00:57:06 +00:00
- tests/software/ucsc/bedgraphtobigwig/**
ucsc/bigwigaverageoverbed:
- software/ucsc/bigwigaverageoverbed/**
- tests/software/ucsc/bigwigaverageoverbed/**
ucsc/wigtobigwig:
- software/ucsc/wigtobigwig/**
- tests/software/ucsc/wigtobigwig/**
unicycler:
- software/unicycler/**
- tests/software/unicycler/**
untar:
- software/untar/**
- tests/software/untar/**
vcftools:
- software/vcftools/**
- tests/software/vcftools/**
yara/index:
- software/yara/index/**
- tests/software/yara/index/**
yara/mapper:
- software/yara/mapper/**
- tests/software/yara/mapper/**