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nf-core_modules/tests/config/pytest_software.yml
Kevin Menden b59e8054e4
fix rseqc/junctionsaturation (#553) 
* bump bcftools filter

* junctionsaturation meta.yml and test

* pytest config entry

* bump bcftools version down again

* fix test

* fix bcftools
2021-07-02 13:31:09 +02:00

788 lines
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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:
- software/bandage/image/**
- tests/software/bandage/image/**
bbmap/bbduk:
- software/bbmap/bbduk/**
- tests/software/bbmap/bbduk/**
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/bamtobed:
- software/bedtools/bamtobed/**
- tests/software/bedtools/bamtobed/**
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:
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- software/bismark/align/**
- software/bismark/deduplicate/**
- software/bismark/methylationextractor/**
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- tests/software/bismark/summary/**
blast/blastn:
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- tests/software/blast/blastn/**
blast/makeblastdb:
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- tests/software/blast/makeblastdb/**
bowtie/align:
- software/bowtie/align/**
- software/bowtie/build/**
- tests/software/bowtie/align/**
bowtie/build:
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- tests/software/bowtie/build_test/**
bowtie2/align:
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- software/bowtie2/build/**
- tests/software/bowtie2/align/**
bowtie2/build:
- software/bowtie2/build/**
- tests/software/bowtie2/build_test/**
bwa/index:
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- 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/**
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:
- 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/**
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/**
gunzip:
- software/gunzip/**
- tests/software/gunzip/**
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/**
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:
- 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/**
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/**
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/**
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:
- software/methyldackel/mbias/**
- tests/software/methyldackel/mbias/**
minia:
- software/minia/**
- tests/software/minia/**
minimap2/align:
- software/minimap2/align/**
- tests/software/minimap2/align/**
minimap2/index:
- software/minimap2/index/**
- tests/software/minimap2/index/**
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:
- software/fastqc/**
- software/multiqc/**
- tests/software/multiqc/**
muscle:
- software/muscle/**
- tests/software/muscle/**
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/**
- 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/**
plasmidid:
- software/plasmidid/**
- tests/software/plasmidid/**
preseq/lcextrap:
- software/preseq/lcextrap/**
- 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:
- 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/preparereference:
- software/rsem/preparereference/**
- tests/software/rsem/preparereference/**
rsem/calculateexpression:
- software/rsem/calculateexpression/**
- tests/software/rsem/calculateexpression/**
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/**
- tests/software/salmon/index/**
salmon/quant:
- software/salmon/quant/**
- tests/software/salmon/quant/**
samtools/faidx:
- software/samtools/faidx/**
- tests/software/samtools/faidx/**
samtools/fastq:
- software/samtools/fastq/**
- tests/software/samtools/fastq/**
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/merge:
- software/samtools/merge/**
- tests/software/samtools/merge/**
samtools/mpileup:
- software/samtools/mpileup/**
- tests/software/samtools/mpileup/**
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/**
seqtk/sample:
- software/seqtk/sample/**
- tests/software/seqtk/sample/**
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:
- software/seqwish/induce/**
- tests/software/seqwish/induce/**
shovill:
- software/shovill/**
- tests/software/shovill/**
snpsites:
- software/snpsites/**
- tests/software/snpsites/**
spades:
- software/spades/**
- tests/software/spades/**
star/align:
- software/star/align/**
- tests/software/star/align/**
star/genomegenerate:
- software/star/genomegenerate/**
- 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:
- software/tabix/tabix/**
- tests/software/tabix/tabix/**
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/bedclip:
- software/ucsc/bedclip/**
- tests/software/ucsc/bedclip/**
ucsc/bedgraphtobigwig:
- software/ucsc/bedgraphtobigwig/**
- 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/**
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