nf-core_modules/tests/config/pytest_software.yml

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adapterremoval:
- software/adapterremoval/**
- tests/software/adapterremoval/**
allelecounter:
- software/allelecounter/**
- tests/software/allelecounter/**
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bandage_image:
- software/bandage/image/**
- tests/software/bandage/image/**
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/**
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bcftools_merge:
- software/bcftools/merge/**
- tests/software/bcftools/merge/**
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bcftools_mpileup:
- software/bcftools/mpileup/**
- tests/software/bcftools/mpileup/**
bcftools_stats:
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- software/bcftools/stats/**
- tests/software/bcftools/stats/**
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bedtools_complement:
- software/bedtools/complement/**
- tests/software/bedtools/complement/**
bedtools_genomecov:
- software/bedtools/genomecov/**
- tests/software/bedtools/genomecov/**
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bedtools_getfasta:
- software/bedtools/getfasta/**
- tests/software/bedtools/getfasta/**
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bedtools_intersect:
- software/bedtools/intersect/**
- tests/software/bedtools/intersect/**
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bedtools_maskfasta:
- software/bedtools/maskfasta/**
- tests/software/bedtools/maskfasta/**
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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/**
bismark_align:
- software/bismark/align/**
- software/bismark/genomepreparation/**
- tests/software/bismark/align/**
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bismark_deduplicate:
- 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/**
bowtie2_align:
- software/bowtie2/align/**
- software/bowtie2/build/**
- tests/software/bowtie2/align/**
bowtie2_build:
- software/bowtie2/build/**
- tests/software/bowtie2/build_test/**
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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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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/**
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bwamem2_index:
- software/bwamem2/index/**
- tests/software/bwamem2/index/**
bwamem2_mem:
- software/bwamem2/mem/**
- tests/software/bwamem2/mem/**
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bwameth_align:
- software/bwameth/align/**
- tests/software/bwameth/align/**
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bwameth_index:
- software/bwameth/index/**
- tests/software/bwameth/index/**
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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>
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cnvkit:
- software/cnvkit/**
- tests/software/cnvkit/**
cutadapt:
- software/cutadapt/**
- tests/software/cutadapt/**
dsh_filterbed:
- software/dsh/filterbed/**
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- tests/software/dsh/filterbed/**
dsh_splitbed:
- software/dsh/splitbed/**
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- tests/software/dsh/splitbed/**
fastp:
- software/fastp/**
- tests/software/fastp/**
fastqc:
- software/fastqc/**
- tests/software/fastqc/**
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_markduplicates:
- software/gatk4/markduplicates/**
- tests/software/gatk4/markduplicates/**
gatk4_mergebamalignment:
- software/gatk4/mergebamalignment/**
- tests/software/gatk4/mergebamalignment/**
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gatk4_mergevcfs:
- software/gatk4/mergevcfs/**
- tests/software/gatk4/mergevcfs/**
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gatk4_revertsam:
- software/gatk4/revertsam/**
- tests/software/gatk4/revertsam/**
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gatk4_samtofastq:
- software/gatk4/samtofastq/**
- tests/software/gatk4/samtofastq/**
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gatk4_splitncigarreads:
- software/gatk4/splitncigarreads/**
- tests/software/gatk4/splitncigarreads/**
gatk4_variantfiltration:
- software/gatk4/variantfiltration/**
- tests/software/gatk4/variantfiltration/**
gffread:
- software/gffread/**
- tests/software/gffread/**
gubbins:
- software/gubbins/**
- tests/software/gubbins/**
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>
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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_annotatepeaks:
- software/homer/annotatepeaks/**
- tests/software/homer/annotatepeaks/**
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ivar_consensus:
- software/ivar/consensus/**
- tests/software/ivar/consensus/**
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ivar_trim:
- software/ivar/trim/**
- tests/software/ivar/trim/**
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ivar_variants:
- software/ivar/variants/**
- tests/software/ivar/variants/**
kallisto_index:
- software/kallisto/index/**
- tests/software/kallisto/index/**
kraken2_run:
- software/kraken2/run/**
- tests/software/kraken2/run/**
methyldackel_extract:
- software/methyldackel/extract/**
- tests/software/methyldackel/extract/**
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methyldackel_mbias:
- software/methyldackel/mbias/**
- tests/software/methyldackel/mbias/**
minia:
- software/minia/**
- tests/software/minia/**
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minimap2_align:
- software/minimap2/align/**
- tests/software/minimap2/align/**
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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/**
optitype:
- software/optitype/**
- tests/software/optitype/**
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/**
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/**
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qualimap_bamqc:
- software/qualimap/bamqc/**
- tests/software/qualimap/bamqc/**
quast:
- software/quast/**
- tests/software/quast/**
salmon_index:
- software/salmon/index/**
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- tests/software/salmon/index/**
salmon_quant:
- software/salmon/quant/**
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- tests/software/salmon/quant/**
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samtools_faidx:
- software/samtools/faidx/**
- tests/software/samtools/faidx/**
samtools_fastq:
- software/samtools/fastq/**
- tests/software/samtools/fastq/**
samtools_flagstat:
- software/samtools/flagstat/**
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- 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/**
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- tests/software/seacr/callpeak/**
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seqkit_split2:
- software/seqkit/split2/**
- tests/software/seqkit/split2/**
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/**
sequenzautils_bam2seqz:
- software/sequenzautils/bam2seqz/**
- tests/software/sequenzautils/bam2seqz/**
sequenzautils_gcwiggle:
- software/sequenzautils/gcwiggle/**
- tests/software/sequenzautils/gcwiggle/**
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seqwish_induce:
- software/seqwish/induce/**
- tests/software/seqwish/induce/**
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shovill:
- software/shovill/**
- tests/software/shovill/**
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:
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- software/stringtie/**
- tests/software/stringtie/**
subread_featurecounts:
- software/subread/featurecounts/**
- tests/software/subread/featurecounts/**
tabix_bgzip:
- software/tabix/bgzip/**
- tests/software/tabix/bgzip/**
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tabix_tabix:
- software/tabix/tabix/**
- tests/software/tabix/tabix/**
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tiddit_sv:
- software/tiddit/sv/**
- tests/software/tiddit/sv/**
trimgalore:
- software/trimgalore/**
- tests/software/trimgalore/**
ucsc_bed12tobigbed:
- software/ucsc/bed12tobigbed/**
- tests/software/ucsc/bed12tobigbed/**
ucsc_bedgraphtobigwig:
- software/ucsc/bedgraphtobigwig/**
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- tests/software/ucsc/bedgraphtobigwig/**
unicycler:
- software/unicycler/**
- tests/software/unicycler/**
untar:
- software/untar/**
- tests/software/untar/**
vcftools:
- software/vcftools/**
- tests/software/vcftools/**
yara:
- software/yara/mapper/**
- tests/software/yara/mapper/**
yara_index:
- software/yara/index/**
- tests/software/yara/index/**