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nf-core_modules/tests/config/pytest_modules.yml
Simon Pearce 78e2e76b24
New module: ichorCNA (#1182) 
* hmmcopy/mapCounter

* update test

* Remove bam tag

* Remove /tmp/ path from test.yml

* Update modules/hmmcopy/mapcounter/meta.yml

Incorporate formatting changes

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/hmmcopy/mapcounter/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update tests/modules/hmmcopy/mapcounter/main.nf

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* ichorCNA run

* Add panel of normals code

* Try and fix tests

* Edit string detection in tests

* Fix linting issues

* Just failing END_VERSIONS

* Fixed versions.yml

* Added DOI

* Optional name for file

* Add when command

* Updated when

* Update modules/ichorcna/createpon/main.nf

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-02-11 16:56:13 +01:00

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abacas:
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- tests/modules/abacas/**
adapterremoval:
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agrvate:
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allelecounter:
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cutadapt:
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damageprofiler:
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dastool/scaffolds2bin:
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deeparg/downloaddata:
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deeparg/predict:
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deeptools/computematrix:
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deeptools/plotfingerprint:
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deeptools/plotheatmap:
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deeptools/plotprofile:
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deepvariant:
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dshbio/splitbed:
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ectyper:
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ensemblvep:
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fastqscan:
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fasttree:
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fgbio/callmolecularconsensusreads:
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fgbio/fastqtobam:
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fgbio/groupreadsbyumi:
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fgbio/sortbam:
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gatk4/applyvqsr:
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gatk4/baserecalibrator:
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gatk4/bedtointervallist:
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gatk4/calculatecontamination:
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gatk4/createsequencedictionary:
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gatk4/createsomaticpanelofnormals:
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gatk4/estimatelibrarycomplexity:
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gatk4/fastqtosam:
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gatk4/filtermutectcalls:
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gatk4/gatherbqsrreports:
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gatk4/genomicsdbimport:
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gatk4/genotypegvcfs:
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gatk4/getpileupsummaries:
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hicap:
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hmmcopy/gccounter:
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hmmcopy/mapcounter:
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hmmcopy/readcounter:
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hmmer/hmmalign:
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homer/annotatepeaks:
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homer/maketagdirectory:
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homer/makeucscfile:
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ichorcna/createpon:
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ichorcna/run:
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idr:
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iqtree:
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ivar/consensus:
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ivar/variants:
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jupyternotebook:
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kallisto/index:
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kallistobustools/ref:
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khmer/normalizebymedian:
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kleborate:
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krona/kronadb:
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krona/ktimporttaxonomy:
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last/dotplot:
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last/mafconvert:
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lissero:
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lofreq/filter:
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lofreq/indelqual:
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macrel/contigs:
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macs2/callpeak:
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- tests/modules/macs2/callpeak/**
malt/build:
- modules/malt/build/**
- tests/modules/malt/build_test/**
malt/run:
- modules/malt/run/**
- tests/modules/malt/run/**
maltextract:
- modules/maltextract/**
- tests/modules/maltextract/**
manta/germline:
- modules/manta/germline/**
- tests/modules/manta/germline/**
manta/somatic:
- modules/manta/somatic/**
- tests/modules/manta/somatic/**
manta/tumoronly:
- modules/manta/tumoronly/**
- tests/modules/manta/tumoronly/**
mapdamage2:
- modules/mapdamage2/**
- tests/modules/mapdamage2/**
mash/dist:
- modules/mash/dist/**
- tests/modules/mash/dist/**
mash/sketch:
- modules/mash/sketch/**
- tests/modules/mash/sketch/**
mashtree:
- modules/mashtree/**
- tests/modules/mashtree/**
maxbin2:
- modules/maxbin2/**
- tests/modules/maxbin2/**
medaka:
- modules/medaka/**
- tests/modules/medaka/**
megahit:
- modules/megahit/**
- tests/modules/megahit/**
meningotype:
- modules/meningotype/**
- tests/modules/meningotype/**
metabat2/jgisummarizebamcontigdepths:
- modules/metabat2/jgisummarizebamcontigdepths/**
- tests/modules/metabat2/jgisummarizebamcontigdepths/**
metabat2/metabat2:
- modules/metabat2/metabat2/**
- tests/modules/metabat2/metabat2/**
metaphlan3:
- modules/metaphlan3/**
- tests/modules/metaphlan3/**
methyldackel/extract:
- modules/methyldackel/extract/**
- tests/modules/methyldackel/extract/**
methyldackel/mbias:
- modules/methyldackel/mbias/**
- tests/modules/methyldackel/mbias/**
minia:
- modules/minia/**
- tests/modules/minia/**
miniasm:
- modules/miniasm/**
- tests/modules/miniasm/**
minimap2/align:
- modules/minimap2/align/**
- tests/modules/minimap2/align/**
minimap2/index:
- modules/minimap2/index/**
- tests/modules/minimap2/index/**
mlst:
- modules/mlst/**
- tests/modules/mlst/**
mosdepth:
- modules/mosdepth/**
- tests/modules/mosdepth/**
msisensor/msi:
- modules/msisensor/msi/**
- tests/modules/msisensor/msi/**
msisensor/scan:
- modules/msisensor/scan/**
- tests/modules/msisensor/scan/**
msisensorpro/msi_somatic:
- modules/msisensorpro/msi_somatic/**
- tests/modules/msisensorpro/msi_somatic/**
msisensorpro/scan:
- modules/msisensorpro/scan/**
- tests/modules/msisensorpro/scan/**
mtnucratio:
- modules/mtnucratio/**
- tests/modules/mtnucratio/**
multiqc:
- modules/fastqc/**
- modules/multiqc/**
- tests/modules/multiqc/**
mummer:
- modules/mummer/**
- tests/modules/mummer/**
muscle:
- modules/muscle/**
- tests/modules/muscle/**
nanolyse:
- modules/nanolyse/**
- tests/modules/nanolyse/**
nanoplot:
- modules/nanoplot/**
- tests/modules/nanoplot/**
ncbigenomedownload:
- modules/ncbigenomedownload/**
- tests/modules/ncbigenomedownload/**
nextclade/datasetget:
- modules/nextclade/datasetget/**
- tests/modules/nextclade/datasetget/**
nextclade/run:
- modules/nextclade/run/**
- tests/modules/nextclade/run/**
ngmaster:
- modules/ngmaster/**
- tests/modules/ngmaster/**
nucmer:
- modules/nucmer/**
- tests/modules/nucmer/**
optitype:
- modules/optitype/**
- tests/modules/optitype/**
pairix:
- modules/pairix/**
- tests/modules/pairix/**
pairtools/dedup:
- modules/pairtools/dedup/**
- tests/modules/pairtools/dedup/**
pairtools/flip:
- modules/pairtools/flip/**
- tests/modules/pairtools/flip/**
pairtools/parse:
- modules/pairtools/parse/**
- tests/modules/pairtools/parse/**
pairtools/restrict:
- modules/pairtools/restrict/**
- tests/modules/pairtools/restrict/**
pairtools/select:
- modules/pairtools/select/**
- tests/modules/pairtools/select/**
pairtools/sort:
- modules/pairtools/sort/**
- tests/modules/pairtools/sort/**
pangolin:
- modules/pangolin/**
- tests/modules/pangolin/**
paraclu:
- modules/paraclu/**
- tests/modules/paraclu/**
pbbam/pbmerge:
- modules/pbbam/pbmerge/**
- tests/modules/pbbam/pbmerge/**
pbccs:
- modules/pbccs/**
- tests/modules/pbccs/**
peddy:
- modules/peddy/**
- tests/modules/peddy/**
phyloflash:
- modules/phyloflash/**
- tests/modules/phyloflash/**
picard/collecthsmetrics:
- modules/picard/collecthsmetrics/**
- tests/modules/picard/collecthsmetrics/**
picard/collectmultiplemetrics:
- modules/picard/collectmultiplemetrics/**
- tests/modules/picard/collectmultiplemetrics/**
picard/collectwgsmetrics:
- modules/picard/collectwgsmetrics/**
- tests/modules/picard/collectwgsmetrics/**
picard/filtersamreads:
- modules/picard/filtersamreads/**
- tests/modules/picard/filtersamreads/**
picard/markduplicates:
- modules/picard/markduplicates/**
- tests/modules/picard/markduplicates/**
picard/mergesamfiles:
- modules/picard/mergesamfiles/**
- tests/modules/picard/mergesamfiles/**
picard/sortsam:
- modules/picard/sortsam/**
- tests/modules/picard/sortsam/**
pirate:
- modules/pirate/**
- tests/modules/pirate/**
plasmidid:
- modules/plasmidid/**
- tests/modules/plasmidid/**
plink/extract:
- modules/plink/extract/**
- tests/modules/plink/extract/**
plink/vcf:
- modules/plink/vcf/**
- tests/modules/plink/vcf/**
plink2/extract:
- modules/plink2/extract/**
- tests/modules/plink2/extract/**
plink2/vcf:
- modules/plink2/vcf/**
- tests/modules/plink2/vcf/**
pmdtools/filter:
- modules/pmdtools/filter/**
- tests/modules/pmdtools/filter/**
porechop:
- modules/porechop/**
- tests/modules/porechop/**
preseq/lcextrap:
- modules/preseq/lcextrap/**
- tests/modules/preseq/lcextrap/**
prodigal:
- modules/prodigal/**
- tests/modules/prodigal/**
prokka:
- modules/prokka/**
- tests/modules/prokka/**
pycoqc:
- modules/pycoqc/**
- tests/modules/pycoqc/**
pydamage/analyze:
- modules/pydamage/analyze/**
- tests/modules/pydamage/analyze/**
pydamage/filter:
- modules/pydamage/filter/**
- tests/modules/pydamage/filter/**
qcat:
- modules/qcat/**
- tests/modules/qcat/**
qualimap/bamqc:
- modules/qualimap/bamqc/**
- tests/modules/qualimap/bamqc/**
quast:
- modules/quast/**
- tests/modules/quast/**
racon:
- modules/racon/**
- tests/modules/racon/**
rapidnj:
- modules/rapidnj/**
- tests/modules/rapidnj/**
rasusa:
- modules/rasusa/**
- tests/modules/rasusa/**
raven:
- modules/raven/**
- tests/modules/raven/**
raxmlng:
- modules/raxmlng/**
- tests/modules/raxmlng/**
rmarkdownnotebook:
- modules/rmarkdownnotebook/**
- tests/modules/rmarkdownnotebook/**
roary:
- modules/roary/**
- tests/modules/roary/**
rsem/calculateexpression:
- modules/rsem/calculateexpression/**
- tests/modules/rsem/calculateexpression/**
rsem/preparereference:
- modules/rsem/preparereference/**
- tests/modules/rsem/preparereference/**
rseqc/bamstat:
- modules/rseqc/bamstat/**
- tests/modules/rseqc/bamstat/**
rseqc/inferexperiment:
- modules/rseqc/inferexperiment/**
- tests/modules/rseqc/inferexperiment/**
rseqc/innerdistance:
- modules/rseqc/innerdistance/**
- tests/modules/rseqc/innerdistance/**
rseqc/junctionannotation:
- modules/rseqc/junctionannotation/**
- tests/modules/rseqc/junctionannotation/**
rseqc/junctionsaturation:
- modules/rseqc/junctionsaturation/**
- tests/modules/rseqc/junctionsaturation/**
rseqc/readdistribution:
- modules/rseqc/readdistribution/**
- tests/modules/rseqc/readdistribution/**
rseqc/readduplication:
- modules/rseqc/readduplication/**
- tests/modules/rseqc/readduplication/**
rseqc/tin:
- modules/rseqc/tin/**
- tests/modules/rseqc/tin/**
salmon/index:
- modules/salmon/index/**
- tests/modules/salmon/index/**
salmon/quant:
- modules/salmon/quant/**
- tests/modules/salmon/quant/**
samblaster:
- modules/samblaster/**
- tests/modules/samblaster/**
samtools/ampliconclip:
- modules/samtools/ampliconclip/**
- tests/modules/samtools/ampliconclip/**
samtools/bam2fq:
- modules/samtools/bam2fq/**
- tests/modules/samtools/bam2fq/**
samtools/depth:
- modules/samtools/depth/**
- tests/modules/samtools/depth/**
samtools/faidx:
- modules/samtools/faidx/**
- tests/modules/samtools/faidx/**
samtools/fastq:
- modules/samtools/fastq/**
- tests/modules/samtools/fastq/**
samtools/fixmate:
- modules/samtools/fixmate/**
- tests/modules/samtools/fixmate/**
samtools/flagstat:
- modules/samtools/flagstat/**
- tests/modules/samtools/flagstat/**
samtools/idxstats:
- modules/samtools/idxstats/**
- tests/modules/samtools/idxstats/**
samtools/index:
- modules/samtools/index/**
- tests/modules/samtools/index/**
samtools/merge:
- modules/samtools/merge/**
- tests/modules/samtools/merge/**
samtools/mpileup:
- modules/samtools/mpileup/**
- tests/modules/samtools/mpileup/**
samtools/sort:
- modules/samtools/sort/**
- tests/modules/samtools/sort/**
samtools/stats:
- modules/samtools/stats/**
- tests/modules/samtools/stats/**
samtools/view:
- modules/samtools/view/**
- tests/modules/samtools/view/**
scoary:
- modules/scoary/**
- tests/modules/scoary/**
seacr/callpeak:
- modules/seacr/callpeak/**
- tests/modules/seacr/callpeak/**
seqkit/split2:
- modules/seqkit/split2/**
- tests/modules/seqkit/split2/**
seqsero2:
- modules/seqsero2/**
- tests/modules/seqsero2/**
seqtk/mergepe:
- modules/seqtk/mergepe/**
- tests/modules/seqtk/mergepe/**
seqtk/sample:
- modules/seqtk/sample/**
- tests/modules/seqtk/sample/**
seqtk/subseq:
- modules/seqtk/subseq/**
- tests/modules/seqtk/subseq/**
sequenzautils/bam2seqz:
- modules/sequenzautils/bam2seqz/**
- tests/modules/sequenzautils/bam2seqz/**
sequenzautils/gcwiggle:
- modules/sequenzautils/gcwiggle/**
- tests/modules/sequenzautils/gcwiggle/**
seqwish/induce:
- modules/seqwish/induce/**
- tests/modules/seqwish/induce/**
shovill:
- modules/shovill/**
- tests/modules/shovill/**
snpdists:
- modules/snpdists/**
- tests/modules/snpdists/**
snpeff:
- modules/snpeff/**
- tests/modules/snpeff/**
snpsift/split:
- modules/snpsift/split/**
- tests/modules/snpsift/split/**
snpsites:
- modules/snpsites/**
- tests/modules/snpsites/**
spades:
- modules/spades/**
- tests/modules/spades/**
spatyper:
- modules/spatyper/**
- tests/modules/spatyper/**
sratools/fasterqdump:
- modules/sratools/fasterqdump/**
- tests/modules/sratools/fasterqdump/**
sratools/prefetch:
- modules/sratools/prefetch/**
- tests/modules/sratools/prefetch/**
staphopiasccmec:
- modules/staphopiasccmec/**
- tests/modules/staphopiasccmec/**
star/align:
- modules/star/align/**
- tests/modules/star/align/**
star/genomegenerate:
- modules/star/genomegenerate/**
- tests/modules/star/genomegenerate/**
strelka/germline:
- modules/strelka/germline/**
- tests/modules/strelka/germline/**
strelka/somatic:
- modules/strelka/somatic/**
- tests/modules/strelka/somatic/**
stringtie/merge:
- modules/stringtie/merge/**
- tests/modules/stringtie/merge/**
stringtie/stringtie:
- modules/stringtie/stringtie/**
- tests/modules/stringtie/stringtie/**
subread/featurecounts:
- modules/subread/featurecounts/**
- tests/modules/subread/featurecounts/**
svdb/merge:
- modules/svdb/merge/**
- tests/modules/svdb/merge/**
svdb/query:
- modules/svdb/query/**
- tests/modules/svdb/query/**
tabix/bgzip:
- modules/tabix/bgzip/**
- tests/modules/tabix/bgzip/**
tabix/bgziptabix:
- modules/tabix/bgziptabix/**
- tests/modules/tabix/bgziptabix/**
tabix/tabix:
- modules/tabix/tabix/**
- tests/modules/tabix/tabix/**
tbprofiler/profile:
- modules/tbprofiler/profile/**
- tests/modules/tbprofiler/profile/**
test/template:
- modules/test/template/**
- tests/modules/test/template/**
tiddit/cov:
- modules/tiddit/cov/**
- tests/modules/tiddit/cov/**
tiddit/sv:
- modules/tiddit/sv/**
- tests/modules/tiddit/sv/**
transdecoder/longorf:
- modules/transdecoder/longorf/**
- tests/modules/transdecoder/longorf/**
transdecoder/predict:
- modules/transdecoder/predict/**
- tests/modules/transdecoder/predict/**
trimgalore:
- modules/trimgalore/**
- tests/modules/trimgalore/**
ucsc/bed12tobigbed:
- modules/ucsc/bed12tobigbed/**
- tests/modules/ucsc/bed12tobigbed/**
ucsc/bedclip:
- modules/ucsc/bedclip/**
- tests/modules/ucsc/bedclip/**
ucsc/bedgraphtobigwig:
- modules/ucsc/bedgraphtobigwig/**
- tests/modules/ucsc/bedgraphtobigwig/**
ucsc/bigwigaverageoverbed:
- modules/ucsc/bigwigaverageoverbed/**
- tests/modules/ucsc/bigwigaverageoverbed/**
ucsc/liftover:
- modules/ucsc/liftover/**
- tests/modules/ucsc/liftover/**
ucsc/wigtobigwig:
- modules/ucsc/wigtobigwig/**
- tests/modules/ucsc/wigtobigwig/**
ultra/pipeline:
- modules/ultra/pipeline/**
- tests/modules/ultra/pipeline/**
unicycler:
- modules/unicycler/**
- tests/modules/unicycler/**
untar:
- modules/untar/**
- tests/modules/untar/**
unzip:
- modules/unzip/**
- tests/modules/unzip/**
variantbam:
- modules/variantbam/**
- tests/modules/variantbam/**
vcfanno:
- modules/vcfanno/**
- tests/modules/vcfanno/**
vcflib/vcfuniq:
- modules/vcflib/vcfuniq/**
- tests/modules/vcflib/vcfuniq/**
vcftools:
- modules/vcftools/**
- tests/modules/vcftools/**
yara/index:
- modules/yara/index/**
- tests/modules/yara/index/**
yara/mapper:
- modules/yara/mapper/**
- tests/modules/yara/mapper/**
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