You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
2522 lines
52 KiB
YAML
2522 lines
52 KiB
YAML
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/**
|
|
|
|
ampir:
|
|
- modules/ampir/**
|
|
- tests/modules/ampir/**
|
|
|
|
amplify/predict:
|
|
- modules/amplify/predict/**
|
|
- tests/modules/amplify/predict/**
|
|
|
|
amps:
|
|
- modules/amps/**
|
|
- tests/modules/amps/**
|
|
|
|
amrfinderplus/run:
|
|
- modules/amrfinderplus/run/**
|
|
- tests/modules/amrfinderplus/run/**
|
|
|
|
amrfinderplus/update:
|
|
- modules/amrfinderplus/update/**
|
|
- tests/modules/amrfinderplus/update/**
|
|
|
|
angsd/docounts:
|
|
- modules/angsd/docounts/**
|
|
- tests/modules/angsd/docounts/**
|
|
|
|
antismash/antismashlite:
|
|
- modules/antismash/antismashlite/**
|
|
- tests/modules/antismash/antismashlite/**
|
|
|
|
antismash/antismashlitedownloaddatabases:
|
|
- modules/antismash/antismashlitedownloaddatabases/**
|
|
- tests/modules/antismash/antismashlitedownloaddatabases/**
|
|
|
|
ariba/getref:
|
|
- modules/ariba/getref/**
|
|
- tests/modules/ariba/getref/**
|
|
|
|
ariba/run:
|
|
- modules/ariba/run/**
|
|
- tests/modules/ariba/run/**
|
|
|
|
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/**
|
|
|
|
ataqv/mkarv:
|
|
- modules/ataqv/mkarv/**
|
|
- tests/modules/ataqv/mkarv/**
|
|
|
|
atlas/call:
|
|
- modules/atlas/call/**
|
|
- tests/modules/atlas/call/**
|
|
|
|
atlas/pmd:
|
|
- modules/atlas/pmd/**
|
|
- tests/modules/atlas/pmd/**
|
|
|
|
atlas/recal:
|
|
- modules/atlas/recal/**
|
|
- tests/modules/atlas/recal/**
|
|
|
|
atlas/splitmerge:
|
|
- modules/atlas/splitmerge/**
|
|
- tests/modules/atlas/splitmerge/**
|
|
|
|
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/**
|
|
|
|
bamtools/stats:
|
|
- modules/bamtools/stats/**
|
|
- tests/modules/bamtools/stats/**
|
|
|
|
bamutil/trimbam:
|
|
- modules/bamutil/trimbam/**
|
|
- tests/modules/bamutil/trimbam/**
|
|
|
|
bandage/image:
|
|
- modules/bandage/image/**
|
|
- tests/modules/bandage/image/**
|
|
|
|
bases2fastq:
|
|
- modules/bases2fastq/**
|
|
- tests/modules/bases2fastq/**
|
|
|
|
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/clumpify:
|
|
- modules/bbmap/clumpify/**
|
|
- tests/modules/bbmap/clumpify/**
|
|
|
|
bbmap/index:
|
|
- modules/bbmap/index/**
|
|
- tests/modules/bbmap/index/**
|
|
|
|
bbmap/pileup:
|
|
- modules/bbmap/pileup/**
|
|
- tests/modules/bbmap/pileup/**
|
|
|
|
bcftools/annotate:
|
|
- modules/bcftools/annotate/**
|
|
- tests/modules/bcftools/annotate/**
|
|
|
|
bcftools/concat:
|
|
- modules/bcftools/concat/**
|
|
- tests/modules/bcftools/concat/**
|
|
|
|
bcftools/consensus:
|
|
- modules/bcftools/consensus/**
|
|
- tests/modules/bcftools/consensus/**
|
|
|
|
bcftools/convert:
|
|
- modules/bcftools/convert/**
|
|
- tests/modules/bcftools/convert/**
|
|
|
|
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/roh:
|
|
- modules/bcftools/roh/**
|
|
- tests/modules/bcftools/roh/**
|
|
|
|
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/**
|
|
|
|
bcl2fastq:
|
|
- modules/bcl2fastq/**
|
|
- tests/modules/bcl2fastq/**
|
|
|
|
bclconvert:
|
|
- modules/bclconvert/**
|
|
- tests/modules/bclconvert/**
|
|
|
|
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/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:
|
|
- modules/bedtools/sort/**
|
|
- tests/modules/bedtools/sort/**
|
|
|
|
bedtools/split:
|
|
- modules/bedtools/split/**
|
|
- tests/modules/bedtools/split/**
|
|
|
|
bedtools/subtract:
|
|
- modules/bedtools/subtract/**
|
|
- tests/modules/bedtools/subtract/**
|
|
|
|
biobambam/bammarkduplicates2:
|
|
- modules/biobambam/bammarkduplicates2/**
|
|
- tests/modules/biobambam/bammarkduplicates2/**
|
|
|
|
biobambam/bammerge:
|
|
- modules/biobambam/bammerge/**
|
|
- tests/modules/biobambam/bammerge/**
|
|
|
|
biobambam/bamsormadup:
|
|
- modules/biobambam/bamsormadup/**
|
|
- tests/modules/biobambam/bamsormadup/**
|
|
|
|
biscuit/align:
|
|
- modules/biscuit/index/**
|
|
- modules/biscuit/align/**
|
|
- tests/modules/biscuit/align/**
|
|
|
|
biscuit/biscuitblaster:
|
|
- modules/biscuit/index/**
|
|
- modules/biscuit/biscuitblaster/**
|
|
- tests/modules/biscuit/biscuitblaster/**
|
|
|
|
biscuit/bsconv:
|
|
- modules/biscuit/index/**
|
|
- modules/biscuit/bsconv/**
|
|
- tests/modules/biscuit/bsconv/**
|
|
|
|
biscuit/epiread:
|
|
- modules/biscuit/index/**
|
|
- modules/biscuit/epiread/**
|
|
- tests/modules/biscuit/epiread/**
|
|
|
|
biscuit/index:
|
|
- modules/biscuit/index/**
|
|
- tests/modules/biscuit/index/**
|
|
|
|
biscuit/mergecg:
|
|
- modules/biscuit/index/**
|
|
- modules/biscuit/mergecg/**
|
|
- tests/modules/biscuit/mergecg/**
|
|
|
|
biscuit/pileup:
|
|
- modules/biscuit/index/**
|
|
- modules/biscuit/pileup/**
|
|
- tests/modules/biscuit/pileup/**
|
|
|
|
biscuit/qc:
|
|
- modules/biscuit/index/**
|
|
- modules/biscuit/qc/**
|
|
- tests/modules/biscuit/qc/**
|
|
|
|
biscuit/vcf2bed:
|
|
- modules/biscuit/vcf2bed/**
|
|
- tests/modules/biscuit/vcf2bed/**
|
|
|
|
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/**
|
|
|
|
blast/tblastn:
|
|
- modules/blast/tblastn/**
|
|
- tests/modules/blast/tblastn/**
|
|
|
|
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:
|
|
- modules/bracken/bracken/**
|
|
- tests/modules/bracken/bracken/**
|
|
|
|
bracken/combinebrackenoutputs:
|
|
- modules/bracken/combinebrackenoutputs/**
|
|
- tests/modules/bracken/combinebrackenoutputs/**
|
|
|
|
busco:
|
|
- modules/busco/**
|
|
- tests/modules/busco/**
|
|
|
|
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/centrifuge:
|
|
- modules/centrifuge/centrifuge/**
|
|
- tests/modules/centrifuge/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/antitarget:
|
|
- modules/cnvkit/antitarget/**
|
|
- tests/modules/cnvkit/antitarget/**
|
|
|
|
cnvkit/batch:
|
|
- modules/cnvkit/batch/**
|
|
- tests/modules/cnvkit/batch/**
|
|
|
|
cnvkit/reference:
|
|
- modules/cnvkit/reference/**
|
|
- tests/modules/cnvkit/reference/**
|
|
|
|
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/**
|
|
|
|
custom/sratoolsncbisettings:
|
|
- modules/custom/sratoolsncbisettings/**
|
|
- tests/modules/custom/sratoolsncbisettings/**
|
|
|
|
cutadapt:
|
|
- modules/cutadapt/**
|
|
- tests/modules/cutadapt/**
|
|
|
|
damageprofiler:
|
|
- modules/damageprofiler/**
|
|
- tests/modules/damageprofiler/**
|
|
|
|
dastool/dastool:
|
|
- modules/dastool/dastool/**
|
|
- tests/modules/dastool/dastool/**
|
|
|
|
dastool/fastatocontig2bin:
|
|
- modules/dastool/fastatocontig2bin/**
|
|
- tests/modules/dastool/fastatocontig2bin/**
|
|
|
|
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/**
|
|
|
|
deepbgc/download:
|
|
- modules/deepbgc/download/**
|
|
- tests/modules/deepbgc/download/**
|
|
|
|
deepbgc/pipeline:
|
|
- modules/deepbgc/pipeline/**
|
|
- tests/modules/deepbgc/pipeline/**
|
|
|
|
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/**
|
|
|
|
eido/convert:
|
|
- modules/eido/convert/**
|
|
- tests/modules/eido/convert/**
|
|
|
|
eido/validate:
|
|
- modules/eido/validate/**
|
|
- tests/modules/eido/validate/**
|
|
|
|
elprep/filter:
|
|
- modules/elprep/filter/**
|
|
- tests/modules/elprep/filter/**
|
|
|
|
elprep/merge:
|
|
- modules/elprep/merge/**
|
|
- tests/modules/elprep/merge/**
|
|
|
|
elprep/split:
|
|
- modules/elprep/split/**
|
|
- tests/modules/elprep/split/**
|
|
|
|
emmtyper:
|
|
- modules/emmtyper/**
|
|
- tests/modules/emmtyper/**
|
|
|
|
endorspy:
|
|
- modules/endorspy/**
|
|
- tests/modules/endorspy/**
|
|
|
|
ensemblvep:
|
|
- modules/ensemblvep/**
|
|
- tests/modules/ensemblvep/**
|
|
|
|
entrezdirect/esearch:
|
|
- modules/entrezdirect/esearch/**
|
|
- tests/modules/entrezdirect/esearch/**
|
|
|
|
entrezdirect/esummary:
|
|
- modules/entrezdirect/esummary/**
|
|
- tests/modules/entrezdirect/esummary/**
|
|
|
|
entrezdirect/xtract:
|
|
- modules/entrezdirect/xtract/**
|
|
- tests/modules/entrezdirect/xtract/**
|
|
|
|
epang:
|
|
- modules/epang/**
|
|
- tests/modules/epang/
|
|
|
|
expansionhunter:
|
|
- modules/expansionhunter/**
|
|
- tests/modules/expansionhunter/**
|
|
|
|
faqcs:
|
|
- modules/faqcs/**
|
|
- tests/modules/faqcs/**
|
|
|
|
fargene:
|
|
- modules/fargene/**
|
|
- tests/modules/fargene/**
|
|
|
|
fastani:
|
|
- modules/fastani/**
|
|
- tests/modules/fastani/**
|
|
|
|
fastawindows:
|
|
- modules/fastawindows/**
|
|
- tests/modules/fastawindows/**
|
|
|
|
fastk/fastk:
|
|
- modules/fastk/fastk/**
|
|
- tests/modules/fastk/fastk/**
|
|
|
|
fastk/histex:
|
|
- modules/fastk/histex/**
|
|
- tests/modules/fastk/histex/**
|
|
|
|
fastk/merge:
|
|
- modules/fastk/merge/**
|
|
- tests/modules/fastk/merge/**
|
|
|
|
fastp:
|
|
- modules/fastp/**
|
|
- tests/modules/fastp/**
|
|
|
|
fastqc:
|
|
- modules/fastqc/**
|
|
- tests/modules/fastqc/**
|
|
|
|
fastqscan:
|
|
- modules/fastqscan/**
|
|
- tests/modules/fastqscan/**
|
|
|
|
fasttree:
|
|
- modules/fasttree/**
|
|
- tests/modules/fasttree/**
|
|
|
|
ffq:
|
|
- modules/ffq/**
|
|
- tests/modules/ffq/**
|
|
|
|
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/**
|
|
|
|
flye:
|
|
- modules/flye/**
|
|
- tests/modules/flye/**
|
|
|
|
fq/lint:
|
|
- modules/fq/lint/**
|
|
- tests/modules/fq/lint/**
|
|
|
|
freebayes:
|
|
- modules/freebayes/**
|
|
- tests/modules/freebayes/**
|
|
|
|
gamma/gamma:
|
|
- modules/gamma/gamma/**
|
|
- tests/modules/gamma/gamma/**
|
|
|
|
gappa/examineassign:
|
|
- modules/gappa/examineassign/**
|
|
- tests/modules/gappa/examineassign/**
|
|
|
|
gappa/examinegraft:
|
|
- modules/gappa/examinegraft/**
|
|
- tests/modules/gappa/examinegraft/**
|
|
|
|
gappa/examineheattree:
|
|
- modules/gappa/examineheattree/**
|
|
- tests/modules/gappa/examineheattree/**
|
|
|
|
gatk/indelrealigner:
|
|
- modules/gatk/indelrealigner/**
|
|
- tests/modules/gatk/indelrealigner/**
|
|
|
|
gatk/realignertargetcreator:
|
|
- modules/gatk/realignertargetcreator/**
|
|
- tests/modules/gatk/realignertargetcreator/**
|
|
|
|
gatk/unifiedgenotyper:
|
|
- modules/gatk/unifiedgenotyper/**
|
|
- tests/modules/gatk/unifiedgenotyper/**
|
|
|
|
gatk4/applybqsr:
|
|
- modules/gatk4/applybqsr/**
|
|
- tests/modules/gatk4/applybqsr/**
|
|
|
|
gatk4/applybqsrspark:
|
|
- modules/gatk4/applybqsrspark/**
|
|
- tests/modules/gatk4/applybqsrspark/**
|
|
|
|
gatk4/applyvqsr:
|
|
- modules/gatk4/applyvqsr/**
|
|
- tests/modules/gatk4/applyvqsr/**
|
|
|
|
gatk4/baserecalibrator:
|
|
- modules/gatk4/baserecalibrator/**
|
|
- tests/modules/gatk4/baserecalibrator/**
|
|
|
|
gatk4/baserecalibratorspark:
|
|
- modules/gatk4/baserecalibratorspark/**
|
|
- tests/modules/gatk4/baserecalibratorspark/**
|
|
|
|
gatk4/bedtointervallist:
|
|
- modules/gatk4/bedtointervallist/**
|
|
- tests/modules/gatk4/bedtointervallist/**
|
|
|
|
gatk4/calculatecontamination:
|
|
- modules/gatk4/calculatecontamination/**
|
|
- tests/modules/gatk4/calculatecontamination/**
|
|
|
|
gatk4/calibratedragstrmodel:
|
|
- modules/gatk4/calibratedragstrmodel/**
|
|
- tests/modules/gatk4/calibratedragstrmodel/**
|
|
|
|
gatk4/cnnscorevariants:
|
|
- modules/gatk4/cnnscorevariants/**
|
|
- tests/modules/gatk4/cnnscorevariants/**
|
|
|
|
gatk4/collectreadcounts:
|
|
- modules/gatk4/collectreadcounts/**
|
|
- tests/modules/gatk4/collectreadcounts/**
|
|
|
|
gatk4/collectsvevidence:
|
|
- modules/gatk4/collectsvevidence/**
|
|
- tests/modules/gatk4/collectsvevidence/**
|
|
|
|
gatk4/combinegvcfs:
|
|
- modules/gatk4/combinegvcfs/**
|
|
- tests/modules/gatk4/combinegvcfs/**
|
|
|
|
gatk4/composestrtablefile:
|
|
- modules/gatk4/composestrtablefile/**
|
|
- tests/modules/gatk4/composestrtablefile/**
|
|
|
|
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/filtervarianttranches:
|
|
- modules/gatk4/filtervarianttranches/**
|
|
- tests/modules/gatk4/filtervarianttranches/**
|
|
|
|
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/leftalignandtrimvariants:
|
|
- modules/gatk4/leftalignandtrimvariants/**
|
|
- tests/modules/gatk4/leftalignandtrimvariants/**
|
|
|
|
gatk4/markduplicates:
|
|
- modules/gatk4/markduplicates/**
|
|
- tests/modules/gatk4/markduplicates/**
|
|
|
|
gatk4/markduplicatesspark:
|
|
- modules/gatk4/markduplicatesspark/**
|
|
- tests/modules/gatk4/markduplicatesspark/**
|
|
|
|
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/printsvevidence:
|
|
- modules/gatk4/printsvevidence/**
|
|
- tests/modules/gatk4/printsvevidence/**
|
|
|
|
gatk4/reblockgvcf:
|
|
- modules/gatk4/reblockgvcf/**
|
|
- tests/modules/gatk4/reblockgvcf/**
|
|
|
|
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/splitintervals:
|
|
- modules/gatk4/splitintervals/**
|
|
- tests/modules/gatk4/splitintervals/**
|
|
|
|
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/**
|
|
|
|
gecco/run:
|
|
- modules/gecco/run/**
|
|
- tests/modules/gecco/run/**
|
|
|
|
genescopefk:
|
|
- modules/genescopefk/**
|
|
- tests/modules/genescopefk/**
|
|
|
|
genmap/index:
|
|
- modules/genmap/index/**
|
|
- tests/modules/genmap/index/**
|
|
|
|
genmap/mappability:
|
|
- modules/genmap/mappability/**
|
|
- tests/modules/genmap/mappability/**
|
|
|
|
genmod/annotate:
|
|
- modules/genmod/annotate/**
|
|
- tests/modules/genmod/annotate/**
|
|
|
|
genmod/compound:
|
|
- modules/genmod/compound/**
|
|
- tests/modules/genmod/compound/**
|
|
|
|
genmod/models:
|
|
- modules/genmod/models/**
|
|
- tests/modules/genmod/models/**
|
|
|
|
genmod/score:
|
|
- modules/genmod/score/**
|
|
- tests/modules/genmod/score/**
|
|
|
|
genomescope2:
|
|
- modules/genomescope2/**
|
|
- tests/modules/genomescope2/**
|
|
|
|
genotyphi/parse:
|
|
- modules/genotyphi/parse/**
|
|
- tests/modules/genotyphi/parse/**
|
|
|
|
genrich:
|
|
- modules/genrich/**
|
|
- tests/modules/genrich/**
|
|
|
|
gfaffix:
|
|
- modules/gfaffix/**
|
|
- tests/modules/gfaffix/**
|
|
|
|
gffread:
|
|
- modules/gffread/**
|
|
- tests/modules/gffread/**
|
|
|
|
glimpse/chunk:
|
|
- modules/glimpse/chunk/**
|
|
- tests/modules/glimpse/chunk/**
|
|
|
|
glnexus:
|
|
- modules/glnexus/**
|
|
- tests/modules/glnexus/**
|
|
|
|
goat/taxonsearch:
|
|
- modules/goat/taxonsearch/**
|
|
- tests/modules/goat/taxonsearch/**
|
|
|
|
graphmap2/align:
|
|
- modules/graphmap2/align/**
|
|
- 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/**
|
|
|
|
gstama/polyacleanup:
|
|
- modules/gstama/polyacleanup/**
|
|
- tests/modules/gstama/polyacleanup/**
|
|
|
|
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/**
|
|
|
|
gvcftools/extractvariants:
|
|
- modules/gvcftools/extractvariants/**
|
|
- tests/modules/gvcftools/extractvariants/**
|
|
|
|
hamronization/abricate:
|
|
- modules/hamronization/abricate/**
|
|
- tests/modules/hamronization/abricate/**
|
|
|
|
hamronization/amrfinderplus:
|
|
- modules/hamronization/amrfinderplus/**
|
|
- tests/modules/hamronization/amrfinderplus/**
|
|
|
|
hamronization/deeparg:
|
|
- modules/hamronization/deeparg/**
|
|
- tests/modules/hamronization/deeparg/**
|
|
|
|
hamronization/fargene:
|
|
- modules/hamronization/fargene/**
|
|
- tests/modules/hamronization/fargene/**
|
|
|
|
hamronization/rgi:
|
|
- modules/hamronization/rgi/**
|
|
- tests/modules/hamronization/rgi/**
|
|
|
|
hamronization/summarize:
|
|
- modules/hamronization/summarize/**
|
|
- tests/modules/hamronization/summarize/**
|
|
|
|
haplocheck:
|
|
- modules/haplocheck/**
|
|
- tests/modules/haplocheck/**
|
|
|
|
haplogrep2/classify:
|
|
- modules/haplogrep2/classify/**
|
|
- tests/modules/haplogrep2/classify/**
|
|
|
|
happy/happy:
|
|
- modules/happy/happy/**
|
|
- tests/modules/happy/happy/**
|
|
|
|
happy/prepy:
|
|
- modules/happy/prepy/**
|
|
- tests/modules/happy/prepy/**
|
|
|
|
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/eslalimask:
|
|
- modules/hmmer/eslalimask/**
|
|
- tests/modules/hmmer/eslalimask/**
|
|
|
|
hmmer/eslreformat:
|
|
- modules/hmmer/eslreformat/**
|
|
- tests/modules/hmmer/eslreformat/**
|
|
|
|
hmmer/hmmalign:
|
|
- modules/hmmer/hmmalign/**
|
|
- tests/modules/hmmer/hmmalign/**
|
|
|
|
hmmer/hmmbuild:
|
|
- modules/hmmer/hmmbuild/**
|
|
- tests/modules/hmmer/hmmbuild/**
|
|
|
|
hmmer/hmmsearch:
|
|
- modules/hmmer/hmmsearch/**
|
|
- tests/modules/hmmer/hmmsearch/**
|
|
|
|
hmtnote:
|
|
- modules/hmtnote/**
|
|
- tests/modules/hmtnote/**
|
|
|
|
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/**
|
|
|
|
instrain/profile:
|
|
- modules/instrain/profile/**
|
|
- tests/modules/instrain/profile/**
|
|
|
|
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/**
|
|
|
|
kaiju/kaiju2krona:
|
|
- modules/kaiju/kaiju2krona/**
|
|
- tests/modules/kaiju/kaiju2krona/**
|
|
|
|
kaiju/kaiju2table:
|
|
- modules/kaiju/kaiju2table/**
|
|
- tests/modules/kaiju/kaiju2table/**
|
|
|
|
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/**
|
|
|
|
kat/hist:
|
|
- modules/kat/hist/**
|
|
- tests/modules/kat/hist/**
|
|
|
|
khmer/normalizebymedian:
|
|
- modules/khmer/normalizebymedian/**
|
|
- tests/modules/khmer/normalizebymedian/**
|
|
|
|
khmer/uniquekmers:
|
|
- modules/khmer/uniquekmers/**
|
|
- tests/modules/khmer/uniquekmers/**
|
|
|
|
kleborate:
|
|
- modules/kleborate/**
|
|
- tests/modules/kleborate/**
|
|
|
|
kraken2/kraken2:
|
|
- modules/kraken2/kraken2/**
|
|
- modules/untar/**
|
|
- tests/modules/kraken2/kraken2/**
|
|
|
|
krakentools/combinekreports:
|
|
- modules/krakentools/combinekreports/**
|
|
- tests/modules/krakentools/combinekreports/**
|
|
|
|
krakentools/kreport2krona:
|
|
- modules/krakentools/kreport2krona/**
|
|
- tests/modules/krakentools/kreport2krona/**
|
|
|
|
krona/kronadb:
|
|
- modules/krona/kronadb/**
|
|
- tests/modules/krona/kronadb/**
|
|
|
|
krona/ktimporttaxonomy:
|
|
- modules/krona/ktimporttaxonomy/**
|
|
- tests/modules/krona/ktimporttaxonomy/**
|
|
|
|
krona/ktimporttext:
|
|
- modules/krona/ktimporttext/**
|
|
- tests/modules/krona/ktimporttext/**
|
|
|
|
krona/ktupdatetaxonomy:
|
|
- modules/krona/ktupdatetaxonomy/**
|
|
- tests/modules/krona/ktupdatetaxonomy/**
|
|
|
|
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/convertinversion:
|
|
- modules/manta/convertinversion/**
|
|
- tests/modules/manta/convertinversion/**
|
|
|
|
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/screen:
|
|
- modules/mash/screen/**
|
|
- tests/modules/mash/screen/**
|
|
|
|
mash/sketch:
|
|
- modules/mash/sketch/**
|
|
- tests/modules/mash/sketch/**
|
|
|
|
mashtree:
|
|
- modules/mashtree/**
|
|
- tests/modules/mashtree/**
|
|
|
|
maxbin2:
|
|
- modules/maxbin2/**
|
|
- tests/modules/maxbin2/**
|
|
|
|
maxquant/lfq:
|
|
- modules/maxquant/lfq/**
|
|
- tests/modules/maxquant/lfq/**
|
|
|
|
mcroni:
|
|
- modules/mcroni/**
|
|
- tests/modules/mcroni/**
|
|
|
|
md5sum:
|
|
- modules/md5sum/**
|
|
- tests/modules/md5sum/**
|
|
|
|
medaka:
|
|
- modules/medaka/**
|
|
- tests/modules/medaka/**
|
|
|
|
megahit:
|
|
- modules/megahit/**
|
|
- tests/modules/megahit/**
|
|
|
|
megan/daa2info:
|
|
- modules/megan/daa2info/**
|
|
- tests/modules/megan/daa2info/**
|
|
|
|
megan/rma2info:
|
|
- modules/megan/rma2info/**
|
|
- tests/modules/megan/rma2info/**
|
|
|
|
meningotype:
|
|
- modules/meningotype/**
|
|
- tests/modules/meningotype/**
|
|
|
|
merqury:
|
|
- modules/merqury/**
|
|
- tests/modules/merqury/**
|
|
|
|
merquryfk/katcomp:
|
|
- modules/merquryfk/katcomp/**
|
|
- tests/modules/merquryfk/katcomp/**
|
|
|
|
merquryfk/katgc:
|
|
- modules/merquryfk/katgc/**
|
|
- tests/modules/merquryfk/katgc/**
|
|
|
|
merquryfk/merquryfk:
|
|
- modules/merquryfk/merquryfk/**
|
|
- tests/modules/merquryfk/merquryfk/**
|
|
|
|
merquryfk/ploidyplot:
|
|
- modules/merquryfk/ploidyplot/**
|
|
- tests/modules/merquryfk/ploidyplot/**
|
|
|
|
meryl/count:
|
|
- modules/meryl/count/**
|
|
- tests/modules/meryl/count/**
|
|
|
|
meryl/histogram:
|
|
- modules/meryl/histogram/**
|
|
- tests/modules/meryl/histogram/**
|
|
|
|
meryl/unionsum:
|
|
- modules/meryl/unionsum/**
|
|
- tests/modules/meryl/unionsum/**
|
|
|
|
metabat2/jgisummarizebamcontigdepths:
|
|
- modules/metabat2/jgisummarizebamcontigdepths/**
|
|
- tests/modules/metabat2/jgisummarizebamcontigdepths/**
|
|
|
|
metabat2/metabat2:
|
|
- modules/metabat2/metabat2/**
|
|
- tests/modules/metabat2/metabat2/**
|
|
|
|
metaphlan3/mergemetaphlantables:
|
|
- modules/metaphlan3/mergemetaphlantables/**
|
|
- tests/modules/metaphlan3/mergemetaphlantables/**
|
|
|
|
metaphlan3/metaphlan3:
|
|
- modules/metaphlan3/metaphlan3/**
|
|
- tests/modules/metaphlan3/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/**
|
|
|
|
motus/downloaddb:
|
|
- modules/motus/downloaddb/**
|
|
- tests/modules/motus/downloaddb/**
|
|
|
|
motus/merge:
|
|
- modules/motus/merge/**
|
|
- tests/modules/motus/merge/**
|
|
|
|
motus/profile:
|
|
- modules/motus/profile/**
|
|
- tests/modules/motus/profile/**
|
|
|
|
msisensor/msi:
|
|
- modules/msisensor/msi/**
|
|
- tests/modules/msisensor/msi/**
|
|
|
|
msisensor/scan:
|
|
- modules/msisensor/scan/**
|
|
- tests/modules/msisensor/scan/**
|
|
|
|
msisensor2/msi:
|
|
- modules/msisensor2/msi/**
|
|
- tests/modules/msisensor2/msi/**
|
|
|
|
msisensor2/scan:
|
|
- modules/msisensor2/scan/**
|
|
- tests/modules/msisensor2/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/**
|
|
|
|
multivcfanalyzer:
|
|
- modules/multivcfanalyzer/**
|
|
- tests/modules/multivcfanalyzer/**
|
|
|
|
mummer:
|
|
- modules/mummer/**
|
|
- tests/modules/mummer/**
|
|
|
|
muscle:
|
|
- modules/muscle/**
|
|
- tests/modules/muscle/**
|
|
|
|
mykrobe/predict:
|
|
- modules/mykrobe/predict/**
|
|
- tests/modules/mykrobe/predict/**
|
|
|
|
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/**
|
|
|
|
nextgenmap:
|
|
- modules/nextgenmap/**
|
|
- tests/modules/nextgenmap/**
|
|
|
|
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/**
|
|
|
|
pasty:
|
|
- modules/pasty/**
|
|
- tests/modules/pasty/**
|
|
|
|
pbbam/pbmerge:
|
|
- modules/pbbam/pbmerge/**
|
|
- tests/modules/pbbam/pbmerge/**
|
|
|
|
pbccs:
|
|
- modules/pbccs/**
|
|
- tests/modules/pbccs/**
|
|
|
|
pbptyper:
|
|
- modules/pbptyper/**
|
|
- tests/modules/pbptyper/**
|
|
|
|
pear:
|
|
- modules/pear/**
|
|
- tests/modules/pear/**
|
|
|
|
peddy:
|
|
- modules/peddy/**
|
|
- tests/modules/peddy/**
|
|
|
|
phantompeakqualtools:
|
|
- modules/phantompeakqualtools/**
|
|
- tests/modules/phantompeakqualtools/**
|
|
|
|
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/crosscheckfingerprints:
|
|
- modules/picard/crosscheckfingerprints/**
|
|
- tests/modules/picard/crosscheckfingerprints/**
|
|
|
|
picard/fastqtosam:
|
|
- modules/picard/fastqtosam/**
|
|
- tests/modules/picard/fastqtosam/**
|
|
|
|
picard/filtersamreads:
|
|
- modules/picard/filtersamreads/**
|
|
- tests/modules/picard/filtersamreads/**
|
|
|
|
picard/fixmateinformation:
|
|
- modules/picard/fixmateinformation/**
|
|
- tests/modules/picard/fixmateinformation/**
|
|
|
|
picard/liftovervcf:
|
|
- modules/picard/liftovervcf/**
|
|
- tests/modules/picard/liftovervcf/**
|
|
|
|
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/**
|
|
|
|
pints/caller:
|
|
- modules/pints/caller/**
|
|
- tests/modules/pints/caller/**
|
|
|
|
pirate:
|
|
- modules/pirate/**
|
|
- tests/modules/pirate/**
|
|
|
|
plasmidfinder:
|
|
- modules/plasmidfinder/**
|
|
- tests/modules/plasmidfinder/**
|
|
|
|
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/**
|
|
|
|
prinseqplusplus:
|
|
- modules/prinseqplusplus/**
|
|
- tests/modules/prinseqplusplus/**
|
|
|
|
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/**
|
|
|
|
rhocall/annotate:
|
|
- modules/rhocall/annotate/**
|
|
- tests/modules/rhocall/annotate/**
|
|
|
|
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/**
|
|
|
|
rtgtools/pedfilter:
|
|
- modules/rtgtools/pedfilter/**
|
|
- tests/modules/rtgtools/pedfilter/**
|
|
|
|
rtgtools/vcfeval:
|
|
- modules/rtgtools/vcfeval/**
|
|
- tests/modules/rtgtools/vcfeval/**
|
|
|
|
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/collate:
|
|
- modules/samtools/collate/**
|
|
- tests/modules/samtools/collate/**
|
|
|
|
samtools/collatefastq:
|
|
- modules/samtools/collatefastq/**
|
|
- tests/modules/samtools/collatefastq/**
|
|
|
|
samtools/convert:
|
|
- modules/samtools/convert/**
|
|
- tests/modules/samtools/convert/**
|
|
|
|
samtools/depth:
|
|
- modules/samtools/depth/**
|
|
- tests/modules/samtools/depth/**
|
|
|
|
samtools/dict:
|
|
- modules/samtools/dict/**
|
|
- tests/modules/samtools/dict/**
|
|
|
|
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/getrg:
|
|
- modules/samtools/getrg/**
|
|
- tests/modules/samtools/getrg/**
|
|
|
|
samtools/idxstats:
|
|
- modules/samtools/idxstats/**
|
|
- tests/modules/samtools/idxstats/**
|
|
|
|
samtools/index:
|
|
- modules/samtools/index/**
|
|
- tests/modules/samtools/index/**
|
|
|
|
samtools/markdup:
|
|
- modules/samtools/markdup/**
|
|
- tests/modules/samtools/markdup/**
|
|
|
|
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/**
|
|
|
|
scramble/clusteranalysis:
|
|
- modules/scramble/clusteranalysis/**
|
|
- tests/modules/scramble/clusteranalysis/**
|
|
|
|
scramble/clusteridentifier:
|
|
- modules/scramble/clusteridentifier/**
|
|
- tests/modules/scramble/clusteridentifier/**
|
|
|
|
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/**
|
|
|
|
seqkit/stats:
|
|
- modules/seqkit/stats/**
|
|
- tests/modules/seqkit/stats/**
|
|
|
|
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/**
|
|
|
|
seroba/run:
|
|
- modules/seroba/run/**
|
|
- tests/modules/seroba/run/**
|
|
|
|
sexdeterrmine:
|
|
- modules/sexdeterrmine/**
|
|
- tests/modules/sexdeterrmine/**
|
|
|
|
shasum:
|
|
- modules/shasum/**
|
|
- tests/modules/shasum/**
|
|
|
|
shigatyper:
|
|
- modules/shigatyper/**
|
|
- tests/modules/shigatyper/**
|
|
|
|
shovill:
|
|
- modules/shovill/**
|
|
- tests/modules/shovill/**
|
|
|
|
sistr:
|
|
- modules/sistr/**
|
|
- tests/modules/sistr/**
|
|
|
|
slimfastq:
|
|
- modules/slimfastq/**
|
|
- tests/modules/slimfastq/**
|
|
|
|
snapaligner/align:
|
|
- modules/snapaligner/align/**
|
|
- tests/modules/snapaligner/align/**
|
|
|
|
snapaligner/index:
|
|
- modules/snapaligner/index/**
|
|
- tests/modules/snapaligner/index/**
|
|
|
|
snippy/core:
|
|
- modules/snippy/core/**
|
|
- tests/modules/snippy/core/**
|
|
|
|
snippy/run:
|
|
- modules/snippy/run/**
|
|
- tests/modules/snippy/run/**
|
|
|
|
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/**
|
|
|
|
somalier/extract:
|
|
- modules/somalier/extract/**
|
|
- tests/modules/somalier/extract/**
|
|
|
|
somalier/relate:
|
|
- modules/somalier/relate/**
|
|
- tests/modules/somalier/relate/**
|
|
|
|
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/**
|
|
|
|
srst2/srst2:
|
|
- modules/srst2/srst2/**
|
|
- tests/modules/srst2/srst2/**
|
|
|
|
ssuissero:
|
|
- modules/ssuissero/**
|
|
- tests/modules/ssuissero/**
|
|
|
|
stadeniolib/scramble:
|
|
- modules/stadeniolib/scramble/**
|
|
- tests/modules/stadeniolib/scramble/**
|
|
|
|
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/**
|
|
|
|
subworkflows/bam_stats_samtools:
|
|
- subworkflows/nf-core/bam_stats_samtools/**
|
|
- tests/subworkflows/nf-core/bam_stats_samtools/**
|
|
|
|
svdb/merge:
|
|
- modules/svdb/merge/**
|
|
- tests/modules/svdb/merge/**
|
|
|
|
svdb/query:
|
|
- modules/svdb/query/**
|
|
- tests/modules/svdb/query/**
|
|
|
|
svtk/standardize:
|
|
- modules/svtk/standardize/**
|
|
- tests/modules/svtk/standardize/**
|
|
|
|
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/**
|
|
|
|
tailfindr:
|
|
- modules/tailfindr/**
|
|
- tests/modules/tailfindr/**
|
|
|
|
tbprofiler/profile:
|
|
- modules/tbprofiler/profile/**
|
|
- tests/modules/tbprofiler/profile/**
|
|
|
|
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/**
|
|
|
|
trimmomatic:
|
|
- modules/trimmomatic/**
|
|
- tests/modules/trimmomatic/**
|
|
|
|
ucsc/bedclip:
|
|
- modules/ucsc/bedclip/**
|
|
- tests/modules/ucsc/bedclip/**
|
|
|
|
ucsc/bedgraphtobigwig:
|
|
- modules/ucsc/bedgraphtobigwig/**
|
|
- tests/modules/ucsc/bedgraphtobigwig/**
|
|
|
|
ucsc/bedtobigbed:
|
|
- modules/ucsc/bedtobigbed/**
|
|
- tests/modules/ucsc/bedtobigbed/**
|
|
|
|
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/align:
|
|
- modules/ultra/align/**
|
|
- tests/modules/ultra/align/**
|
|
|
|
ultra/index:
|
|
- modules/ultra/index/**
|
|
- tests/modules/ultra/index/**
|
|
|
|
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/**
|
|
|
|
vardictjava:
|
|
- modules/vardictjava/**
|
|
- tests/modules/vardictjava/**
|
|
|
|
variantbam:
|
|
- modules/variantbam/**
|
|
- tests/modules/variantbam/**
|
|
|
|
vcf2db:
|
|
- modules/vcf2db/**
|
|
- tests/modules/vcf2db/**
|
|
|
|
vcf2maf:
|
|
- modules/vcf2maf/**
|
|
- tests/modules/vcf2maf/**
|
|
|
|
vcfanno:
|
|
- modules/vcfanno/**
|
|
- tests/modules/vcfanno/**
|
|
|
|
vcflib/vcfuniq:
|
|
- modules/vcflib/vcfuniq/**
|
|
- tests/modules/vcflib/vcfuniq/**
|
|
|
|
vcftools:
|
|
- modules/vcftools/**
|
|
- tests/modules/vcftools/**
|
|
|
|
vsearch/sintax:
|
|
- modules/vsearch/sintax/**
|
|
- tests/modules/vsearch/sintax/**
|
|
|
|
vsearch/usearchglobal:
|
|
- modules/vsearch/usearchglobal/**
|
|
- tests/modules/vsearch/usearchglobal/**
|
|
|
|
whamg:
|
|
- modules/whamg/**
|
|
- tests/modules/whamg/**
|
|
|
|
yara/index:
|
|
- modules/yara/index/**
|
|
- tests/modules/yara/index/**
|
|
|
|
yara/mapper:
|
|
- modules/yara/mapper/**
|
|
- tests/modules/yara/mapper/**
|