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nf-core_modules/tests/config/pytest_software.yml
Ravneet Bhuller 8a2a9f7e81
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 15:27:30 -07:00

396 lines
8.5 KiB
YAML
Executable file
Raw Blame History

adapterremoval:
- software/adapterremoval/**
- tests/software/adapterremoval/**
bandage_image:
- software/bandage/image/**
- tests/software/bandage/image/**
bcftools_consensus:
- software/bcftools/consensus/**
- tests/software/bcftools/consensus/**
bcftools_filter:
- software/bcftools/filter/**
- tests/software/bcftools/filter/**
bcftools_isec:
- software/bcftools/isec/**
- tests/software/bcftools/isec/**
bcftools_merge:
- software/bcftools/merge/**
- tests/software/bcftools/merge/**
bcftools_mpileup:
- software/bcftools/mpileup/**
- tests/software/bcftools/mpileup/**
bcftools_stats:
- software/bcftools/stats/**
- tests/software/bcftools/stats/**
bedtools_complement:
- software/bedtools/complement/**
- tests/software/bedtools/complement/**
bedtools_genomecov:
- software/bedtools/genomecov/**
- tests/software/bedtools/genomecov/**
bedtools_getfasta:
- software/bedtools/getfasta/**
- tests/software/bedtools/getfasta/**
bedtools_intersect:
- software/bedtools/intersect/**
- tests/software/bedtools/intersect/**
bedtools_maskfasta:
- software/bedtools/maskfasta/**
- tests/software/bedtools/maskfasta/**
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/**
bismark_deduplicate:
- software/bismark/deduplicate/**
- tests/software/bismark/deduplicate/**
bismark_genomepreparation:
- software/bismark/genomepreparation/**
- tests/software/bismark/genomepreparation/**
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/**
bowtie_align:
- software/bowtie/align/**
- software/bowtie/build/**
- tests/software/bowtie/align/**
bowtie_build:
- software/bowtie/build/**
- tests/software/bowtie/build_test/**
bwa_index:
- software/bwa/index/**
- tests/software/bwa/index/**
bwa_mem:
- software/bwa/mem/**
- tests/software/bwa/mem/**
bwamem2_index:
- software/bwamem2/index/**
- tests/software/bwamem2/index/**
bwamem2_mem:
- software/bwamem2/mem/**
- tests/software/bwamem2/mem/**
bwameth_align:
- software/bwameth/align/**
- tests/software/bwameth/align/**
bwameth_index:
- software/bwameth/index/**
- tests/software/bwameth/index/**
cat_fastq:
- software/cat/fastq/**
- tests/software/cat/fastq/**
cnvkit:
- software/cnvkit/**
- tests/software/cnvkit/**
cutadapt:
- software/cutadapt/**
- tests/software/cutadapt/**
dsh_filterbed:
- software/dsh/filterbed/**
- tests/software/dsh/filterbed/**
dsh_splitbed:
- software/dsh/splitbed/**
- tests/software/dsh/splitbed/**
fastp:
- software/fastp/**
- tests/software/fastp/**
fastqc:
- software/fastqc/**
- tests/software/fastqc/**
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_mergebamalignment:
- software/gatk4/mergebamalignment/**
- tests/software/gatk4/mergebamalignment/**
gatk4_mergevcfs:
- software/gatk4/mergevcfs/**
- tests/software/gatk4/mergevcfs/**
gatk4_revertsam:
- software/gatk4/revertsam/**
- tests/software/gatk4/revertsam/**
gatk4_samtofastq:
- software/gatk4/samtofastq/**
- tests/software/gatk4/samtofastq/**
gatk4_splitncigarreads:
- software/gatk4/splitncigarreads/**
- tests/software/gatk4/splitncigarreads/**
gatk4_variantfiltration:
- software/gatk4/variantfiltration/**
- tests/software/gatk4/variantfiltration/**
gffread:
- software/gffread/**
- tests/software/gffread/**
gunzip:
- software/gunzip/**
- tests/software/gunzip/**
ivar_consensus:
- software/ivar/consensus/**
- tests/software/ivar/consensus/**
ivar_trim:
- software/ivar/trim/**
- tests/software/ivar/trim/**
ivar_variants:
- software/ivar/variants/**
- tests/software/ivar/variants/**
kraken2_run:
- software/kraken2/run/**
- tests/software/kraken2/run/**
methyldackel_extract:
- software/methyldackel/extract/**
- tests/software/methyldackel/extract/**
methyldackel_mbias:
- software/methyldackel/mbias/**
- tests/software/methyldackel/mbias/**
minia:
- software/minia/**
- tests/software/minia/**
minimap2_align:
- software/minimap2/align/**
- tests/software/minimap2/align/**
mosdepth:
- software/mosdepth/**
- tests/software/mosdepth/**
multiqc:
- software/fastqc/**
- software/multiqc/**
- tests/software/multiqc/**
pangolin:
- software/pangolin/**
- tests/software/pangolin/**
picard_collectmultiplemetrics:
- software/picard/collectmultiplemetrics/**
- tests/software/picard/collectmultiplemetrics/**
picard_collectwgsmetrics:
- software/picard/collectwgsmetrics/**
- tests/software/picard/collectwgsmetrics/**
picard_markduplicates:
- software/picard/markduplicates/**
- tests/software/picard/markduplicates/**
picard_mergesamfiles:
- software/picard/mergesamfiles/**
- tests/software/picard/mergesamfiles/**
preseq_lcextrap:
- software/preseq/lcextrap/**
- tests/software/preseq/lcextrap/**
qualimap_bamqc:
- software/qualimap/bamqc/**
- tests/software/qualimap/bamqc/**
quast:
- software/quast/**
- tests/software/quast/**
salmon_index:
- software/salmon/index/**
- tests/software/salmon/index/**
salmon_quant:
- software/salmon/quant/**
- tests/software/salmon/quant/**
samtools_faidx:
- software/samtools/faidx/**
- tests/software/samtools/faidx/**
samtools_flagstat:
- software/samtools/flagstat/**
- tests/software/samtools/flagstat/**
samtools_idxstats:
- software/samtools/idxstats/**
- tests/software/samtools/idxstats/**
samtools_index:
- software/samtools/index/**
- tests/software/samtools/index/**
samtools_mpileup:
- software/samtools/mpileup/**
- tests/software/samtools/mpileup/**
samtools_merge:
- software/samtools/merge/**
- tests/software/samtools/merge/**
samtools_sort:
- software/samtools/sort/**
- tests/software/samtools/sort/**
samtools_stats:
- software/samtools/stats/**
- tests/software/samtools/stats/**
samtools_view:
- software/samtools/view/**
- tests/software/samtools/view/**
seacr_callpeak:
- software/seacr/callpeak/**
- tests/software/seacr/callpeak/**
seqkit_split2:
- software/seqkit/split2/**
- tests/software/seqkit/split2/**
sequenza_wiggle:
- software/sequenza/wiggle/**
- tests/software/sequenza/wiggle/**
seqwish_induce:
- software/seqwish/induce/**
- tests/software/seqwish/induce/**
spades:
- software/spades/**
- tests/software/spades/**
star_align:
- software/star/align/**
- tests/software/star/align/**
star_genomegenerate:
- software/star/genomegenerate/**
- tests/software/star/genomegenerate/**
stringtie:
- software/stringtie/**
- tests/software/stringtie/**
tabix_bgzip:
- software/tabix/bgzip/**
- tests/software/tabix/bgzip/**
tabix_tabix:
- software/tabix/tabix/**
- tests/software/tabix/tabix/**
tiddit_sv:
- software/tiddit/sv/**
- tests/software/tiddit/sv/**
trimgalore:
- software/trimgalore/**
- tests/software/trimgalore/**
ucsc_bedgraphtobigwig:
- software/ucsc/bedgraphtobigwig/**
- tests/software/ucsc/bedgraphtobigwig/**
unicycler:
- software/unicycler/**
- tests/software/unicycler/**
untar:
- software/untar/**
- tests/software/untar/**
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