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nf-core_modules/tests/config/pytest_modules.yml
James A. Fellows Yates 1a26d48104
module: picard sortsam (#603) 
* Add picard/sortsam module

* Fix container links

* Changes after code review

* Input meta in the right place
2021-07-21 13:48:07 +02:00

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abacas:
- modules/abacas/**
- tests/modules/abacas/**
adapterremoval:
- modules/adapterremoval/**
- tests/modules/adapterremoval/**
allelecounter:
- modules/allelecounter/**
- tests/modules/allelecounter/**
artic/guppyplex:
- modules/artic/guppyplex/**
- tests/modules/artic/guppyplex/**
artic/minion:
- modules/artic/minion/**
- tests/modules/artic/minion/**
bandage/image:
- modules/bandage/image/**
- tests/modules/bandage/image/**
bbmap/bbduk:
- modules/bbmap/bbduk/**
- tests/modules/bbmap/bbduk/**
bcftools/consensus:
- modules/bcftools/consensus/**
- tests/modules/bcftools/consensus/**
bcftools/filter:
- modules/bcftools/filter/**
- tests/modules/bcftools/filter/**
bcftools/isec:
- modules/bcftools/isec/**
- tests/modules/bcftools/isec/**
bcftools/merge:
- modules/bcftools/merge/**
- tests/modules/bcftools/merge/**
bcftools/mpileup:
- modules/bcftools/mpileup/**
- tests/modules/bcftools/mpileup/**
bcftools/stats:
- modules/bcftools/stats/**
- tests/modules/bcftools/stats/**
bedtools/bamtobed:
- modules/bedtools/bamtobed/**
- tests/modules/bedtools/bamtobed/**
bedtools/complement:
- modules/bedtools/complement/**
- tests/modules/bedtools/complement/**
bedtools/genomecov:
- modules/bedtools/genomecov/**
- tests/modules/bedtools/genomecov/**
bedtools/getfasta:
- modules/bedtools/getfasta/**
- tests/modules/bedtools/getfasta/**
bedtools/intersect:
- modules/bedtools/intersect/**
- tests/modules/bedtools/intersect/**
bedtools/maskfasta:
- modules/bedtools/maskfasta/**
- tests/modules/bedtools/maskfasta/**
bedtools/merge:
- modules/bedtools/merge/**
- tests/modules/bedtools/merge/**
bedtools/slop:
- modules/bedtools/slop/**
- tests/modules/bedtools/slop/**
bedtools/sort:
- modules/bedtools/sort/**
- tests/modules/bedtools/sort/**
bedtools/subtract:
- modules/bedtools/subtract/**
- tests/modules/bedtools/subtract/**
bismark/align:
- modules/bismark/align/**
- modules/bismark/genomepreparation/**
- tests/modules/bismark/align/**
bismark/deduplicate:
- modules/bismark/deduplicate/**
- tests/modules/bismark/deduplicate/**
bismark/genomepreparation:
- modules/bismark/genomepreparation/**
- tests/modules/bismark/genomepreparation/**
bismark/methylationextractor:
- modules/bismark/methylationextractor/**
- modules/bismark/genomepreparation/**
- tests/modules/bismark/methylationextractor/**
bismark/report:
- modules/bismark/genomepreparation/**
- modules/bismark/align/**
- modules/bismark/deduplicate/**
- modules/bismark/methylationextractor/**
- modules/bismark/report/**
- tests/modules/bismark/report/**
bismark/summary:
- modules/bismark/genomepreparation/**
- modules/bismark/align/**
- modules/bismark/deduplicate/**
- modules/bismark/methylationextractor/**
- modules/bismark/summary/**
- tests/modules/bismark/summary/**
blast/blastn:
- modules/blast/blastn/**
- tests/modules/blast/blastn/**
blast/makeblastdb:
- modules/blast/makeblastdb/**
- tests/modules/blast/makeblastdb/**
bowtie/align:
- modules/bowtie/align/**
- modules/bowtie/build/**
- tests/modules/bowtie/align/**
bowtie/build:
- modules/bowtie/build/**
- tests/modules/bowtie/build_test/**
bowtie2/align:
- modules/bowtie2/align/**
- modules/bowtie2/build/**
- tests/modules/bowtie2/align/**
bowtie2/build:
- modules/bowtie2/build/**
- tests/modules/bowtie2/build_test/**
bwa/index:
- modules/bwa/index/**
- tests/modules/bwa/index/**
bwa/mem:
- modules/bwa/mem/**
- tests/modules/bwa/mem/**
bwamem2/index:
- modules/bwamem2/index/**
- tests/modules/bwamem2/index/**
bwamem2/mem:
- modules/bwamem2/mem/**
- tests/modules/bwamem2/mem/**
bwameth/align:
- modules/bwameth/align/**
- tests/modules/bwameth/align/**
bwameth/index:
- modules/bwameth/index/**
- tests/modules/bwameth/index/**
cat/fastq:
- modules/cat/fastq/**
- tests/modules/cat/fastq/**
cnvkit:
- modules/cnvkit/**
- tests/modules/cnvkit/**
cooler/digest:
- modules/cooler/digest/**
- tests/modules/cooler/digest/**
cooler/dump:
- modules/cooler/dump/**
- tests/modules/cooler/dump/**
cutadapt:
- modules/cutadapt/**
- tests/modules/cutadapt/**
damageprofiler:
- modules/damageprofiler/**
- tests/modules/damageprofiler/**
deeptools/computematrix:
- modules/deeptools/computematrix/**
- tests/modules/deeptools/computematrix/**
deeptools/plotfingerprint:
- modules/deeptools/plotfingerprint/**
- tests/modules/deeptools/plotfingerprint/**
deeptools/plotheatmap:
- modules/deeptools/plotheatmap/**
- tests/modules/deeptools/plotheatmap/**
deeptools/plotprofile:
- modules/deeptools/plotprofile/**
- tests/modules/deeptools/plotprofile/**
delly/call:
- modules/delly/call/**
- tests/modules/delly/call/**
dshbio/filterbed:
- modules/dshbio/filterbed/**
- tests/modules/dshbio/filterbed/**
dshbio/filtergff3:
- modules/dshbio/filtergff3/**
- tests/modules/dshbio/filtergff3/**
dshbio/splitbed:
- modules/dshbio/splitbed/**
- tests/modules/dshbio/splitbed/**
dshbio/splitgff3:
- modules/dshbio/splitgff3/**
- tests/modules/dshbio/splitgff3/**
ensemblvep:
- modules/ensemblvep/**
- tests/modules/ensemblvep/**
fastp:
- modules/fastp/**
- tests/modules/fastp/**
fastqc:
- modules/fastqc/**
- tests/modules/fastqc/**
fasttree:
- modules/fasttree/**
- tests/modules/fasttree/**
fgbio/callmolecularconsensusreads:
- modules/fgbio/callmolecularconsensusreads/**
- tests/modules/fgbio/callmolecularconsensusreads/**
fgbio/sortbam:
- modules/fgbio/sortbam/**
- tests/modules/fgbio/sortbam/**
flash:
- modules/flash/**
- tests/modules/flash/**
gatk4/applybqsr:
- modules/gatk4/applybqsr/**
- tests/modules/gatk4/applybqsr/**
gatk4/baserecalibrator:
- modules/gatk4/baserecalibrator/**
- tests/modules/gatk4/baserecalibrator/**
gatk4/bedtointervallist:
- modules/gatk4/bedtointervallist/**
- tests/modules/gatk4/bedtointervallist/**
gatk4/createsequencedictionary:
- modules/gatk4/createsequencedictionary/**
- tests/modules/gatk4/createsequencedictionary/**
gatk4/fastqtosam:
- modules/gatk4/fastqtosam/**
- tests/modules/gatk4/fastqtosam/**
gatk4/haplotypecaller:
- modules/gatk4/haplotypecaller/**
- tests/modules/gatk4/haplotypecaller/**
gatk4/intervallisttools:
- modules/gatk4/intervallisttools/**
- tests/modules/gatk4/intervallisttools/**
gatk4/markduplicates:
- modules/gatk4/markduplicates/**
- tests/modules/gatk4/markduplicates/**
gatk4/mergebamalignment:
- modules/gatk4/mergebamalignment/**
- tests/modules/gatk4/mergebamalignment/**
gatk4/mergevcfs:
- modules/gatk4/mergevcfs/**
- tests/modules/gatk4/mergevcfs/**
gatk4/revertsam:
- modules/gatk4/revertsam/**
- tests/modules/gatk4/revertsam/**
gatk4/samtofastq:
- modules/gatk4/samtofastq/**
- tests/modules/gatk4/samtofastq/**
gatk4/splitncigarreads:
- modules/gatk4/splitncigarreads/**
- tests/modules/gatk4/splitncigarreads/**
gatk4/variantfiltration:
- modules/gatk4/variantfiltration/**
- tests/modules/gatk4/variantfiltration/**
genmap/index:
- modules/genmap/index/**
- tests/modules/genmap/index/**
genmap/mappability:
- modules/genmap/mappability/**
- tests/modules/genmap/mappability/**
gffread:
- modules/gffread/**
- tests/modules/gffread/**
graphmap2/align:
- modules/graphmap2/align/**
- tests/modules/graphmap2/align/**
graphmap2/index:
- modules/graphmap2/index/**
- tests/modules/graphmap2/index/**
gubbins:
- modules/gubbins/**
- tests/modules/gubbins/**
gunzip:
- modules/gunzip/**
- tests/modules/gunzip/**
hifiasm:
- modules/hifiasm/**
- tests/modules/hifiasm/**
hisat2/align:
- modules/hisat2/align/**
- modules/hisat2/build/**
- modules/hisat2/extractsplicesites/**
- tests/modules/hisat2/align/**
hisat2/build:
- modules/hisat2/build/**
- modules/hisat2/extractsplicesites/**
- tests/modules/hisat2/build_test/**
hisat2/extractsplicesites:
- modules/hisat2/extractsplicesites/**
- tests/modules/hisat2/extractsplicesites/**
hmmer/hmmalign:
- modules/hmmer/hmmalign/**
- tests/modules/hmmer/hmmalign/**
homer/annotatepeaks:
- modules/homer/annotatepeaks/**
- tests/modules/homer/annotatepeaks/**
iqtree:
- modules/iqtree/**
- tests/modules/iqtree/**
ivar/consensus:
- modules/ivar/consensus/**
- tests/modules/ivar/consensus/**
ivar/trim:
- modules/ivar/trim/**
- tests/modules/ivar/trim/**
ivar/variants:
- modules/ivar/variants/**
- tests/modules/ivar/variants/**
kallisto/index:
- modules/kallisto/index/**
- tests/modules/kallisto/index/**
kallistobustools/count:
- modules/kallistobustools/count/**
- tests/modules/kallistobustools/count/**
kallistobustools/ref:
- modules/kallistobustools/ref/**
- tests/modules/kallistobustools/ref/**
kraken2/kraken2:
- modules/kraken2/kraken2/**
- modules/untar/**
- tests/modules/kraken2/kraken2/**
last/dotplot:
- modules/last/dotplot/**
- tests/modules/last/dotplot/**
last/lastal:
- modules/last/lastal/**
- tests/modules/last/lastal/**
last/lastdb:
- modules/last/lastdb/**
- tests/modules/last/lastdb/**
last/mafconvert:
- modules/last/mafconvert/**
- tests/modules/last/mafconvert/**
last/mafswap:
- modules/last/mafswap/**
- tests/modules/last/mafswap/**
last/postmask:
- modules/last/postmask/**
- tests/modules/last/postmask/**
last/split:
- modules/last/split/**
- tests/modules/last/split/**
last/train:
- modules/last/train/**
- tests/modules/last/train/**
lofreq/call:
- modules/lofreq/call/**
- tests/modules/lofreq/call/**
lofreq/callparallel:
- modules/lofreq/callparallel/**
- tests/modules/lofreq/callparallel/**
lofreq/filter:
- modules/lofreq/filter/**
- tests/modules/lofreq/filter/**
lofreq/indelqual:
- modules/lofreq/indelqual/**
- tests/modules/lofreq/indelqual/**
mash/sketch:
- modules/mash/sketch/**
- tests/modules/mash/sketch/**
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/**
minimap2/align:
- modules/minimap2/align/**
- tests/modules/minimap2/align/**
minimap2/index:
- modules/minimap2/index/**
- tests/modules/minimap2/index/**
mosdepth:
- modules/mosdepth/**
- tests/modules/mosdepth/**
msisensor/msi:
- modules/msisensor/msi/**
- tests/modules/msisensor/msi/**
msisensor/scan:
- modules/msisensor/scan/**
- tests/modules/msisensor/scan/**
multiqc:
- modules/fastqc/**
- modules/multiqc/**
- tests/modules/multiqc/**
muscle:
- modules/muscle/**
- tests/modules/muscle/**
nanolyse:
- modules/nanolyse/**
- tests/modules/nanolyse/**
nanoplot:
- modules/nanoplot/**
- tests/modules/nanoplot/**
nextclade:
- modules/nextclade/**
- tests/modules/nextclade/**
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/**
picard/collectmultiplemetrics:
- modules/picard/collectmultiplemetrics/**
- tests/modules/picard/collectmultiplemetrics/**
picard/collectwgsmetrics:
- modules/picard/collectwgsmetrics/**
- tests/modules/picard/collectwgsmetrics/**
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/**
plasmidid:
- modules/plasmidid/**
- tests/modules/plasmidid/**
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/**
qcat:
- modules/qcat/**
- tests/modules/qcat/**
qualimap/bamqc:
- modules/qualimap/bamqc/**
- tests/modules/qualimap/bamqc/**
quast:
- modules/quast/**
- tests/modules/quast/**
rapidnj:
- modules/rapidnj/**
- tests/modules/rapidnj/**
rasusa:
- modules/rasusa/**
- tests/modules/rasusa/**
raxmlng:
- modules/raxmlng/**
- tests/modules/raxmlng/**
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/**
salmon/index:
- modules/salmon/index/**
- tests/modules/salmon/index/**
salmon/quant:
- modules/salmon/quant/**
- tests/modules/salmon/quant/**
samtools/ampliconclip:
- modules/samtools/ampliconclip/**
- tests/modules/samtools/ampliconclip/**
samtools/faidx:
- modules/samtools/faidx/**
- tests/modules/samtools/faidx/**
samtools/fastq:
- modules/samtools/fastq/**
- tests/modules/samtools/fastq/**
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/**
seacr/callpeak:
- modules/seacr/callpeak/**
- tests/modules/seacr/callpeak/**
seqkit/split2:
- modules/seqkit/split2/**
- tests/modules/seqkit/split2/**
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/**
snpeff:
- modules/snpeff/**
- tests/modules/snpeff/**
snpsites:
- modules/snpsites/**
- tests/modules/snpsites/**
spades:
- modules/spades/**
- tests/modules/spades/**
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/**
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/**
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/**
tiddit/sv:
- modules/tiddit/sv/**
- tests/modules/tiddit/sv/**
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/wigtobigwig:
- modules/ucsc/wigtobigwig/**
- tests/modules/ucsc/wigtobigwig/**
unicycler:
- modules/unicycler/**
- tests/modules/unicycler/**
untar:
- modules/untar/**
- tests/modules/untar/**
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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