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nf-core_modules/tests/config/pytest_modules.yml
Tanja Normark 1f483d9203
Add kaiju_kaiju module (#1448) 
* Added kaiju_kaiju module

* Update modules/kaiju/kaiju/main.nf

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

* Update modules/kaiju/kaiju/main.nf

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

* Update modules/kaiju/kaiju/meta.yml

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

* Update keywords

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

* Update output file naming

* Update output file naming

* update spacing for lint

* Update input file patterns

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

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-03-28 14:28:50 +02:00

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abacas:
- modules/abacas/**
- tests/modules/abacas/**
abricate/run:
- modules/abricate/run/**
- tests/modules/abricate/run/**
abricate/summary:
- modules/abricate/summary/**
- tests/modules/abricate/summary/**
adapterremoval:
- modules/adapterremoval/**
- tests/modules/adapterremoval/**
adapterremovalfixprefix:
- modules/adapterremovalfixprefix/**
- tests/modules/adapterremovalfixprefix/**
agrvate:
- modules/agrvate/**
- tests/modules/agrvate/**
allelecounter:
- modules/allelecounter/**
- tests/modules/allelecounter/**
amps:
- modules/amps/**
- tests/modules/amps/**
amrfinderplus/run:
- modules/amrfinderplus/run/**
- tests/modules/amrfinderplus/run/**
amrfinderplus/update:
- modules/amrfinderplus/update/**
- tests/modules/amrfinderplus/update/**
arriba:
- modules/arriba/**
- tests/modules/arriba/**
artic/guppyplex:
- modules/artic/guppyplex/**
- tests/modules/artic/guppyplex/**
artic/minion:
- modules/artic/minion/**
- tests/modules/artic/minion/**
ascat:
- modules/ascat/**
- tests/modules/ascat/**
assemblyscan:
- modules/assemblyscan/**
- tests/modules/assemblyscan/**
ataqv/ataqv:
- modules/ataqv/ataqv/**
- tests/modules/ataqv/ataqv/**
bakta:
- modules/bakta/**
- tests/modules/bakta/**
bamaligncleaner:
- modules/bamaligncleaner/**
- tests/modules/bamaligncleaner/**
bamcmp:
- modules/bamcmp/**
- tests/modules/bamcmp/**
bamtools/convert:
- modules/bamtools/convert/**
- tests/modules/bamtools/convert/**
bamtools/split:
- modules/bamtools/split/**
- tests/modules/bamtools/split/**
bamutil/trimbam:
- modules/bamutil/trimbam/**
- tests/modules/bamutil/trimbam/**
bandage/image:
- modules/bandage/image/**
- tests/modules/bandage/image/**
bbmap/align:
- modules/bbmap/align/**
- tests/modules/bbmap/align/**
bbmap/bbduk:
- modules/bbmap/bbduk/**
- tests/modules/bbmap/bbduk/**
bbmap/bbsplit:
- modules/bbmap/bbsplit/**
- tests/modules/bbmap/bbsplit/**
bbmap/index:
- modules/bbmap/index/**
- tests/modules/bbmap/index/**
bbmap/pileup:
- modules/bbmap/pileup/**
- tests/modules/bbmap/pileup/**
bcftools/annotate:
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- tests/modules/bcftools/annotate/**
bcftools/concat:
- modules/bcftools/concat/**
- tests/modules/bcftools/concat/**
bcftools/consensus:
- modules/bcftools/consensus/**
- tests/modules/bcftools/consensus/**
bcftools/filter:
- modules/bcftools/filter/**
- tests/modules/bcftools/filter/**
bcftools/index:
- modules/bcftools/index/**
- tests/modules/bcftools/index**
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/norm:
- modules/bcftools/norm/**
- tests/modules/bcftools/norm/**
bcftools/query:
- modules/bcftools/query/**
- tests/modules/bcftools/query/**
bcftools/reheader:
- modules/bcftools/reheader/**
- tests/modules/bcftools/reheader/**
bcftools/sort:
- modules/bcftools/sort/**
- tests/modules/bcftools/sort/**
bcftools/stats:
- modules/bcftools/stats/**
- tests/modules/bcftools/stats/**
bcftools/view:
- modules/bcftools/view/**
- tests/modules/bcftools/view/**
bedtools/bamtobed:
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- 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/makewindows:
- modules/bedtools/makewindows/**
- tests/modules/bedtools/makewindows/**
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:
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- tests/modules/bedtools/sort/**
bedtools/subtract:
- modules/bedtools/subtract/**
- tests/modules/bedtools/subtract/**
biobambam/bammarkduplicates2:
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- tests/modules/biobambam/bammarkduplicates2/**
biscuit/align:
- modules/biscuit/index/**
- modules/biscuit/align/**
- tests/modules/biscuit/align/**
biscuit/biscuitblaster:
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- modules/biscuit/biscuitblaster/**
- tests/modules/biscuit/biscuitblaster/**
biscuit/bsconv:
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biscuit/epiread:
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- modules/biscuit/epiread/**
- tests/modules/biscuit/epiread/**
biscuit/index:
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biscuit/mergecg:
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biscuit/pileup:
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biscuit/qc:
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biscuit/vcf2bed:
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bismark/align:
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- tests/modules/bismark/align/**
bismark/deduplicate:
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- 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:
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- modules/bismark/align/**
- modules/bismark/deduplicate/**
- modules/bismark/methylationextractor/**
- modules/bismark/report/**
- tests/modules/bismark/report/**
bismark/summary:
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- 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/**
bracken/bracken:
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- tests/modules/bracken/bracken/**
bwa/aln:
- modules/bwa/aln/**
- tests/modules/bwa/aln/**
bwa/index:
- modules/bwa/index/**
- tests/modules/bwa/index/**
bwa/mem:
- modules/bwa/mem/**
- tests/modules/bwa/mem/**
bwa/sampe:
- modules/bwa/sampe/**
- tests/modules/bwa/sampe/**
bwa/samse:
- modules/bwa/samse/**
- tests/modules/bwa/samse/**
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/cat:
- modules/cat/cat/**
- tests/modules/cat/cat/**
cat/fastq:
- modules/cat/fastq/**
- tests/modules/cat/fastq/**
cellranger/count:
- modules/cellranger/count/**
- tests/modules/cellranger/count/**
- modules/cellranger/mkref/**
- tests/modules/cellranger/mkref/**
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
cellranger/gtf:
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
cellranger/mkfastq:
- modules/cellranger/mkfastq/**
- tests/modules/cellranger/mkfastq/**
cellranger/mkgtf:
- modules/cellranger/mkgtf/**
- tests/modules/cellranger/mkgtf/**
cellranger/mkref:
- modules/cellranger/mkref/**
- tests/modules/cellranger/mkref/**
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
centrifuge:
- modules/centrifuge/**
- tests/modules/centrifuge/**
checkm/lineagewf:
- modules/checkm/lineagewf/**
- tests/modules/checkm/lineagewf/**
chromap/chromap:
- modules/chromap/chromap/**
- tests/modules/chromap/chromap/**
chromap/index:
- modules/chromap/index/**
- tests/modules/chromap/index/**
clonalframeml:
- modules/clonalframeml/**
- tests/modules/clonalframeml/**
cmseq/polymut:
- modules/cmseq/polymut/**
- tests/modules/cmseq/polymut/**
cnvkit/batch:
- modules/cnvkit/batch/**
- tests/modules/cnvkit/batch/**
controlfreec/assesssignificance:
- modules/controlfreec/assesssignificance/**
- tests/modules/controlfreec/assesssignificance/**
controlfreec/freec:
- modules/controlfreec/freec/**
- tests/modules/controlfreec/freec/**
controlfreec/freec2bed:
- modules/controlfreec/freec2bed/**
- tests/modules/controlfreec/freec2bed/**
controlfreec/freec2circos:
- modules/controlfreec/freec2circos/**
- tests/modules/controlfreec/freec2circos/**
controlfreec/makegraph:
- modules/controlfreec/makegraph/**
- tests/modules/controlfreec/makegraph/**
cooler/cload:
- modules/cooler/cload/**
- tests/modules/cooler/cload/**
cooler/digest:
- modules/cooler/digest/**
- tests/modules/cooler/digest/**
cooler/dump:
- modules/cooler/dump/**
- tests/modules/cooler/dump/**
cooler/merge:
- modules/cooler/merge/**
- tests/modules/cooler/merge/**
cooler/zoomify:
- modules/cooler/zoomify/**
- tests/software/cooler/zoomify/**
csvtk/concat:
- modules/csvtk/concat/**
- tests/modules/csvtk/concat/**
csvtk/split:
- modules/csvtk/split/**
- tests/modules/csvtk/split/**
custom/dumpsoftwareversions:
- modules/custom/dumpsoftwareversions/**
- tests/modules/custom/dumpsoftwareversions/**
custom/getchromsizes:
- modules/custom/getchromsizes/**
- tests/modules/custom/getchromsizes/**
cutadapt:
- modules/cutadapt/**
- tests/modules/cutadapt/**
damageprofiler:
- modules/damageprofiler/**
- tests/modules/damageprofiler/**
dastool/dastool:
- modules/dastool/dastool/**
- tests/modules/dastool/dastool/**
dastool/scaffolds2bin:
- modules/dastool/scaffolds2bin/**
- tests/modules/dastool/scaffolds2bin/**
dedup:
- modules/dedup/**
- tests/modules/dedup/**
deeparg/downloaddata:
- modules/deeparg/downloaddata/**
- tests/modules/deeparg/downloaddata/**
deeparg/predict:
- modules/deeparg/predict/**
- tests/modules/deeparg/predict/**
deeptools/bamcoverage:
- modules/deeptools/bamcoverage/**
- tests/modules/deeptools/bamcoverage/**
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/**
deepvariant:
- modules/deepvariant/**
- tests/modules/deepvariant/**
delly/call:
- modules/delly/call/**
- tests/modules/delly/call/**
diamond/blastp:
- modules/diamond/blastp/**
- tests/modules/diamond/blastp/**
diamond/blastx:
- modules/diamond/blastx/**
- tests/modules/diamond/blastx/**
diamond/makedb:
- modules/diamond/makedb/**
- tests/modules/diamond/makedb/**
dragmap/align:
- modules/dragmap/align/**
- tests/modules/dragmap/align/**
dragmap/hashtable:
- modules/dragmap/hashtable/**
- tests/modules/dragmap/hashtable/**
dragonflye:
- modules/dragonflye/**
- tests/modules/dragonflye/**
dshbio/exportsegments:
- modules/dshbio/exportsegments/**
- tests/modules/dshbio/exportsegments/**
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/**
ectyper:
- modules/ectyper/**
- tests/modules/ectyper/**
emmtyper:
- modules/emmtyper/**
- tests/modules/emmtyper/**
ensemblvep:
- modules/ensemblvep/**
- tests/modules/ensemblvep/**
expansionhunter:
- modules/expansionhunter/**
- tests/modules/expansionhunter/**
faqcs:
- modules/faqcs/**
- tests/modules/faqcs/**
fargene:
- modules/fargene/**
- tests/modules/fargene/**
fastani:
- modules/fastani/**
- tests/modules/fastani/**
fastp:
- modules/fastp/**
- tests/modules/fastp/**
fastqc:
- modules/fastqc/**
- tests/modules/fastqc/**
fastqscan:
- modules/fastqscan/**
- tests/modules/fastqscan/**
fasttree:
- modules/fasttree/**
- tests/modules/fasttree/**
fgbio/callmolecularconsensusreads:
- modules/fgbio/callmolecularconsensusreads/**
- tests/modules/fgbio/callmolecularconsensusreads/**
fgbio/fastqtobam:
- modules/fgbio/fastqtobam/**
- tests/modules/fgbio/fastqtobam/**
fgbio/groupreadsbyumi:
- modules/fgbio/groupreadsbyumi/**
- tests/modules/fgbio/groupreadsbyumi/**
fgbio/sortbam:
- modules/fgbio/sortbam/**
- tests/modules/fgbio/sortbam/**
filtlong:
- modules/filtlong/**
- tests/modules/filtlong/**
flash:
- modules/flash/**
- tests/modules/flash/**
freebayes:
- modules/freebayes/**
- tests/modules/freebayes/**
gatk4/applybqsr:
- modules/gatk4/applybqsr/**
- tests/modules/gatk4/applybqsr/**
gatk4/applyvqsr:
- modules/gatk4/applyvqsr/**
- tests/modules/gatk4/applyvqsr/**
gatk4/baserecalibrator:
- modules/gatk4/baserecalibrator/**
- tests/modules/gatk4/baserecalibrator/**
gatk4/bedtointervallist:
- modules/gatk4/bedtointervallist/**
- tests/modules/gatk4/bedtointervallist/**
gatk4/calculatecontamination:
- modules/gatk4/calculatecontamination/**
- tests/modules/gatk4/calculatecontamination/**
gatk4/combinegvcfs:
- modules/gatk4/combinegvcfs/**
- tests/modules/gatk4/combinegvcfs/**
gatk4/createsequencedictionary:
- modules/gatk4/createsequencedictionary/**
- tests/modules/gatk4/createsequencedictionary/**
gatk4/createsomaticpanelofnormals:
- modules/gatk4/createsomaticpanelofnormals/**
- tests/modules/gatk4/createsomaticpanelofnormals/**
gatk4/estimatelibrarycomplexity:
- modules/gatk4/estimatelibrarycomplexity/**
- tests/modules/gatk4/estimatelibrarycomplexity/**
gatk4/fastqtosam:
- modules/gatk4/fastqtosam/**
- tests/modules/gatk4/fastqtosam/**
gatk4/filtermutectcalls:
- modules/gatk4/filtermutectcalls/**
- tests/modules/gatk4/filtermutectcalls/**
gatk4/gatherbqsrreports:
- modules/gatk4/gatherbqsrreports/**
- tests/modules/gatk4/gatherbqsrreports/**
gatk4/gatherpileupsummaries:
- modules/gatk4/gatherpileupsummaries/**
- tests/modules/gatk4/gatherpileupsummaries/**
gatk4/genomicsdbimport:
- modules/gatk4/genomicsdbimport/**
- tests/modules/gatk4/genomicsdbimport/**
gatk4/genotypegvcfs:
- modules/gatk4/genotypegvcfs/**
- tests/modules/gatk4/genotypegvcfs/**
gatk4/getpileupsummaries:
- modules/gatk4/getpileupsummaries/**
- tests/modules/gatk4/getpileupsummaries/**
gatk4/haplotypecaller:
- modules/gatk4/haplotypecaller/**
- tests/modules/gatk4/haplotypecaller/**
gatk4/indexfeaturefile:
- modules/gatk4/indexfeaturefile/**
- tests/modules/gatk4/indexfeaturefile/**
gatk4/intervallisttobed:
- modules/gatk4/intervallisttobed/**
- tests/modules/gatk4/intervallisttobed/**
gatk4/intervallisttools:
- modules/gatk4/intervallisttools/**
- tests/modules/gatk4/intervallisttools/**
gatk4/learnreadorientationmodel:
- modules/gatk4/learnreadorientationmodel/**
- tests/modules/gatk4/learnreadorientationmodel/**
gatk4/markduplicates:
- modules/gatk4/markduplicates/**
- tests/modules/gatk4/markduplicates/**
gatk4/mergebamalignment:
- modules/gatk4/mergebamalignment/**
- tests/modules/gatk4/mergebamalignment/**
gatk4/mergemutectstats:
- modules/gatk4/mergemutectstats/**
- tests/modules/gatk4/mergemutectstats/**
gatk4/mergevcfs:
- modules/gatk4/mergevcfs/**
- tests/modules/gatk4/mergevcfs/**
gatk4/mutect2:
- modules/gatk4/mutect2/**
- tests/modules/gatk4/mutect2/**
gatk4/revertsam:
- modules/gatk4/revertsam/**
- tests/modules/gatk4/revertsam/**
gatk4/samtofastq:
- modules/gatk4/samtofastq/**
- tests/modules/gatk4/samtofastq/**
gatk4/selectvariants:
- modules/gatk4/selectvariants/**
- tests/modules/gatk4/selectvariants/**
gatk4/splitncigarreads:
- modules/gatk4/splitncigarreads/**
- tests/modules/gatk4/splitncigarreads/**
gatk4/variantfiltration:
- modules/gatk4/variantfiltration/**
- tests/modules/gatk4/variantfiltration/**
gatk4/variantrecalibrator:
- modules/gatk4/variantrecalibrator/**
- tests/modules/gatk4/variantrecalibrator/**
genmap/index:
- modules/genmap/index/**
- tests/modules/genmap/index/**
genmap/mappability:
- modules/genmap/mappability/**
- tests/modules/genmap/mappability/**
genrich:
- modules/genrich/**
- tests/modules/genrich/**
gffread:
- modules/gffread/**
- tests/modules/gffread/**
glnexus:
- modules/glnexus/**
- tests/modules/glnexus/**
graphmap2/align:
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- tests/modules/graphmap2/align/**
graphmap2/index:
- modules/graphmap2/index/**
- tests/modules/graphmap2/index/**
gstama/collapse:
- modules/gstama/collapse/**
- tests/modules/gstama/collapse/**
gstama/merge:
- modules/gstama/merge/**
- tests/modules/gstama/merge/**
gtdbtk/classifywf:
- modules/gtdbtk/classifywf/**
- tests/modules/gtdbtk/classifywf/**
gubbins:
- modules/gubbins/**
- tests/modules/gubbins/**
gunc/downloaddb:
- modules/gunc/downloaddb/**
- tests/modules/gunc/downloaddb/**
gunc/run:
- modules/gunc/run/**
- tests/modules/gunc/run/**
gunzip:
- modules/gunzip/**
- tests/modules/gunzip/**
hamronization/deeparg:
- modules/hamronization/deeparg/**
- tests/modules/hamronization/deeparg/**
hamronization/summarize:
- modules/hamronization/summarize/**
- tests/modules/hamronization/summarize/**
hicap:
- modules/hicap/**
- tests/modules/hicap/**
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/**
hmmcopy/gccounter:
- modules/hmmcopy/gccounter/**
- tests/modules/hmmcopy/gccounter/**
hmmcopy/generatemap:
- modules/hmmcopy/generatemap/**
- tests/modules/hmmcopy/generatemap/**
hmmcopy/mapcounter:
- modules/hmmcopy/mapcounter/**
- tests/modules/hmmcopy/mapcounter/**
hmmcopy/readcounter:
- modules/hmmcopy/readcounter/**
- tests/modules/hmmcopy/readcounter/**
hmmer/hmmalign:
- modules/hmmer/hmmalign/**
- tests/modules/hmmer/hmmalign/**
hmmer/hmmsearch:
- modules/hmmer/hmmsearch/**
- tests/modules/hmmer/hmmsearch/**
homer/annotatepeaks:
- modules/homer/annotatepeaks/**
- tests/modules/homer/annotatepeaks/**
homer/findpeaks:
- modules/homer/findpeaks/**
- modules/homer/maketagdirectory/**
- tests/modules/homer/findpeaks/**
homer/maketagdirectory:
- modules/homer/maketagdirectory/**
- tests/modules/homer/maketagdirectory/**
homer/makeucscfile:
- modules/homer/makeucscfile/**
- tests/modules/homer/makeucscfile/**
homer/pos2bed:
- modules/homer/pos2bed/**
- modules/homer/maketagdirectory/**
- modules/homer/findpeaks/**
- tests/modules/homer/pos2bed/**
hpsuissero:
- modules/hpsuissero/**
- tests/modules/hpsuissero/**
ichorcna/createpon:
- modules/ichorcna/createpon/**
- tests/modules/ichorcna/createpon/**
ichorcna/run:
- modules/ichorcna/run/**
- tests/modules/ichorcna/run/**
idr:
- modules/idr/**
- tests/modules/idr/**
imputeme/vcftoprs:
- modules/imputeme/vcftoprs/**
- tests/modules/imputeme/vcftoprs/**
iqtree:
- modules/iqtree/**
- tests/modules/iqtree/**
ismapper:
- modules/ismapper/**
- tests/modules/ismapper/**
isoseq3/cluster:
- modules/isoseq3/cluster/**
- tests/modules/isoseq3/cluster/**
isoseq3/refine:
- modules/isoseq3/refine/**
- tests/modules/isoseq3/refine/**
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/**
jupyternotebook:
- modules/jupyternotebook/**
- tests/modules/jupyternotebook/**
kaiju/kaiju:
- modules/kaiju/kaiju/**
- tests/modules/kaiju/kaiju/**
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/**
khmer/normalizebymedian:
- modules/khmer/normalizebymedian/**
- tests/modules/khmer/normalizebymedian/**
kleborate:
- modules/kleborate/**
- tests/modules/kleborate/**
kraken2/kraken2:
- modules/kraken2/kraken2/**
- modules/untar/**
- tests/modules/kraken2/kraken2/**
krona/kronadb:
- modules/krona/kronadb/**
- tests/modules/krona/kronadb/**
krona/ktimporttaxonomy:
- modules/krona/ktimporttaxonomy/**
- tests/modules/krona/ktimporttaxonomy/**
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/**
leehom:
- modules/leehom/**
- tests/modules/leehom/**
legsta:
- modules/legsta/**
- tests/modules/legsta/**
lima:
- modules/lima/**
- tests/modules/lima/**
lissero:
- modules/lissero/**
- tests/modules/lissero/**
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/**
macrel/contigs:
- modules/macrel/contigs/**
- tests/modules/macrel/contigs/**
macs2/callpeak:
- modules/macs2/callpeak/**
- tests/modules/macs2/callpeak/**
mafft:
- modules/mafft/**
- tests/modules/mafft/**
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/**
mobsuite/recon:
- modules/mobsuite/recon/**
- tests/modules/mobsuite/recon/**
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/**
ngscheckmate/ncm:
- modules/ngscheckmate/ncm/**
- tests/modules/ngscheckmate/ncm/**
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/**
panaroo/run:
- modules/panaroo/run/**
- tests/modules/panaroo/run/**
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/addorreplacereadgroups:
- modules/picard/addorreplacereadgroups/**
- tests/modules/picard/addorreplacereadgroups/**
picard/cleansam:
- modules/picard/cleansam/**
- tests/modules/picard/cleansam/**
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/createsequencedictionary:
- modules/picard/createsequencedictionary/**
- tests/modules/picard/createsequencedictionary/**
picard/filtersamreads:
- modules/picard/filtersamreads/**
- tests/modules/picard/filtersamreads/**
picard/fixmateinformation:
- modules/picard/fixmateinformation/**
- tests/modules/picard/fixmateinformation/**
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/**
picard/sortvcf:
- modules/picard/sortvcf/**
- tests/modules/picard/sortvcf/**
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/score:
- modules/plink2/score/**
- tests/modules/plink2/score/**
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/ccurve:
- modules/preseq/ccurve/**
- tests/modules/preseq/ccurve/**
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/**
qualimap/bamqccram:
- modules/qualimap/bamqccram/**
- tests/modules/qualimap/bamqccram/**
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/**
rgi/main:
- modules/rgi/main/**
- tests/modules/rgi/main/**
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/pair:
- modules/seqkit/pair/**
- tests/modules/seqkit/pair/**
seqkit/replace:
- modules/seqkit/replace/**
- tests/modules/seqkit/replace/**
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/rename:
- modules/seqtk/rename/**
- tests/modules/seqtk/rename/**
seqtk/sample:
- modules/seqtk/sample/**
- tests/modules/seqtk/sample/**
seqtk/seq:
- modules/seqtk/seq/**
- tests/modules/seqtk/seq/**
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/**
sistr:
- modules/sistr/**
- tests/modules/sistr/**
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/**
sourmash/sketch:
- modules/sourmash/sketch/**
- tests/modules/sourmash/sketch/**
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/**
ssuissero:
- modules/ssuissero/**
- tests/modules/ssuissero/**
staphopiasccmec:
- modules/staphopiasccmec/**
- tests/modules/staphopiasccmec/**
star/align:
- modules/star/align/**
- tests/modules/star/align/**
star/genomegenerate:
- modules/star/genomegenerate/**
- tests/modules/star/genomegenerate/**
stranger:
- modules/stranger/**
- tests/modules/stranger/**
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/**
umitools/dedup:
- modules/umitools/dedup/**
- modules/umitools/extract/**
- tests/modules/umitools/dedup/**
umitools/extract:
- modules/umitools/extract/**
- tests/modules/umitools/extract/**
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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