mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
ca53f7525b
* Added diamond * minor tweaks & yml fix * Fixed spacing issues due to failing lint * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/makedb/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastx/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/modules/diamond/blastp/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/diamond/blastp/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
1004 lines
21 KiB
YAML
1004 lines
21 KiB
YAML
abacas:
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- modules/abacas/**
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- tests/modules/abacas/**
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adapterremoval:
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- modules/adapterremoval/**
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- tests/modules/adapterremoval/**
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agrvate:
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- modules/agrvate/**
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- tests/modules/agrvate/**
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allelecounter:
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- modules/allelecounter/**
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- tests/modules/allelecounter/**
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arriba:
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- modules/arriba/**
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- tests/modules/arriba/**
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artic/guppyplex:
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- modules/artic/guppyplex/**
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- tests/modules/artic/guppyplex/**
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artic/minion:
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- modules/artic/minion/**
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- tests/modules/artic/minion/**
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bamaligncleaner:
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- modules/bamaligncleaner/**
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- tests/modules/bamaligncleaner/**
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bandage/image:
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- modules/bandage/image/**
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- tests/modules/bandage/image/**
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bbmap/align:
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- modules/bbmap/align/**
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- tests/modules/bbmap/align/**
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bbmap/bbduk:
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- modules/bbmap/bbduk/**
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- tests/modules/bbmap/bbduk/**
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bbmap/index:
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- modules/bbmap/index/**
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- tests/modules/bbmap/index/**
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bcftools/concat:
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- modules/bcftools/concat/**
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- tests/modules/bcftools/concat/**
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bcftools/consensus:
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- modules/bcftools/consensus/**
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- tests/modules/bcftools/consensus/**
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bcftools/filter:
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- modules/bcftools/filter/**
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- tests/modules/bcftools/filter/**
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bcftools/isec:
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- modules/bcftools/isec/**
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- tests/modules/bcftools/isec/**
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bcftools/merge:
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- modules/bcftools/merge/**
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- tests/modules/bcftools/merge/**
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bcftools/mpileup:
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- modules/bcftools/mpileup/**
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- tests/modules/bcftools/mpileup/**
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bcftools/norm:
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- modules/bcftools/norm/**
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- tests/modules/bcftools/norm/**
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bcftools/query:
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- modules/bcftools/query/**
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- tests/modules/bcftools/query/**
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bcftools/reheader:
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- modules/bcftools/reheader/**
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- tests/modules/bcftools/reheader/**
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bcftools/stats:
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- modules/bcftools/stats/**
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- tests/modules/bcftools/stats/**
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bcftools/view:
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- modules/bcftools/view/**
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- tests/modules/bcftools/view/**
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bedtools/bamtobed:
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- modules/bedtools/bamtobed/**
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- tests/modules/bedtools/bamtobed/**
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bedtools/complement:
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- modules/bedtools/complement/**
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- tests/modules/bedtools/complement/**
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bedtools/genomecov:
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- modules/bedtools/genomecov/**
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- tests/modules/bedtools/genomecov/**
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bedtools/getfasta:
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- modules/bedtools/getfasta/**
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- tests/modules/bedtools/getfasta/**
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bedtools/intersect:
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- modules/bedtools/intersect/**
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- tests/modules/bedtools/intersect/**
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bedtools/makewindows:
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- modules/bedtools/makewindows/**
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- tests/modules/bedtools/makewindows/**
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bedtools/maskfasta:
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- modules/bedtools/maskfasta/**
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- tests/modules/bedtools/maskfasta/**
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bedtools/merge:
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- modules/bedtools/merge/**
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- tests/modules/bedtools/merge/**
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bedtools/slop:
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- modules/bedtools/slop/**
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- tests/modules/bedtools/slop/**
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bedtools/sort:
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- modules/bedtools/sort/**
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- tests/modules/bedtools/sort/**
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bedtools/subtract:
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- modules/bedtools/subtract/**
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- tests/modules/bedtools/subtract/**
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bismark/align:
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- modules/bismark/align/**
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- modules/bismark/genomepreparation/**
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- tests/modules/bismark/align/**
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bismark/deduplicate:
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- modules/bismark/deduplicate/**
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- tests/modules/bismark/deduplicate/**
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bismark/genomepreparation:
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- modules/bismark/genomepreparation/**
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- tests/modules/bismark/genomepreparation/**
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bismark/methylationextractor:
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- modules/bismark/methylationextractor/**
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- modules/bismark/genomepreparation/**
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- tests/modules/bismark/methylationextractor/**
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bismark/report:
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- modules/bismark/genomepreparation/**
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- modules/bismark/align/**
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- modules/bismark/deduplicate/**
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- modules/bismark/methylationextractor/**
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- modules/bismark/report/**
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- tests/modules/bismark/report/**
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bismark/summary:
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- modules/bismark/genomepreparation/**
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- modules/bismark/align/**
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- modules/bismark/deduplicate/**
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- modules/bismark/methylationextractor/**
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- modules/bismark/summary/**
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- tests/modules/bismark/summary/**
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blast/blastn:
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- modules/blast/blastn/**
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- tests/modules/blast/blastn/**
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blast/makeblastdb:
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- modules/blast/makeblastdb/**
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- tests/modules/blast/makeblastdb/**
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bowtie/align:
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- modules/bowtie/align/**
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- modules/bowtie/build/**
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- tests/modules/bowtie/align/**
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bowtie/build:
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- modules/bowtie/build/**
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- tests/modules/bowtie/build_test/**
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bowtie2/align:
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- modules/bowtie2/align/**
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- modules/bowtie2/build/**
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- tests/modules/bowtie2/align/**
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bowtie2/build:
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- modules/bowtie2/build/**
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- tests/modules/bowtie2/build_test/**
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bwa/aln:
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- modules/bwa/aln/**
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- tests/modules/bwa/aln/**
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bwa/index:
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- modules/bwa/index/**
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- tests/modules/bwa/index/**
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bwa/mem:
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- modules/bwa/mem/**
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- tests/modules/bwa/mem/**
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bwa/sampe:
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- modules/bwa/sampe/**
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- tests/modules/bwa/sampe/**
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bwa/samse:
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- modules/bwa/samse/**
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- tests/modules/bwa/samse/**
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bwamem2/index:
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- modules/bwamem2/index/**
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- tests/modules/bwamem2/index/**
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bwamem2/mem:
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- modules/bwamem2/mem/**
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- tests/modules/bwamem2/mem/**
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bwameth/align:
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- modules/bwameth/align/**
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- tests/modules/bwameth/align/**
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bwameth/index:
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- modules/bwameth/index/**
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- tests/modules/bwameth/index/**
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cat/cat:
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- modules/cat/cat/**
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- tests/modules/cat/cat/**
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cat/fastq:
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- modules/cat/fastq/**
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- tests/modules/cat/fastq/**
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chromap/chromap:
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- modules/chromap/chromap/**
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- tests/modules/chromap/chromap/**
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chromap/index:
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- modules/chromap/index/**
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- tests/modules/chromap/index/**
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cnvkit:
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- modules/cnvkit/**
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- tests/modules/cnvkit/**
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cooler/digest:
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- modules/cooler/digest/**
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- tests/modules/cooler/digest/**
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cooler/dump:
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- modules/cooler/dump/**
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- tests/modules/cooler/dump/**
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cutadapt:
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- modules/cutadapt/**
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- tests/modules/cutadapt/**
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damageprofiler:
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- modules/damageprofiler/**
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- tests/modules/damageprofiler/**
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deeptools/computematrix:
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- modules/deeptools/computematrix/**
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- tests/modules/deeptools/computematrix/**
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deeptools/plotfingerprint:
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- modules/deeptools/plotfingerprint/**
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- tests/modules/deeptools/plotfingerprint/**
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deeptools/plotheatmap:
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- modules/deeptools/plotheatmap/**
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- tests/modules/deeptools/plotheatmap/**
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deeptools/plotprofile:
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- modules/deeptools/plotprofile/**
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- tests/modules/deeptools/plotprofile/**
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delly/call:
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- modules/delly/call/**
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- tests/modules/delly/call/**
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diamond/blastx:
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- modules/diamond/blastx/**
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- tests/modules/diamond/blastx/**
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diamond/blastp:
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- modules/diamond/blastp/**
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- tests/modules/diamond/blastp/**
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diamond/makedb:
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- modules/diamond/makedb/**
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- tests/modules/diamond/makedb/**
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dragonflye:
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- modules/dragonflye/**
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- tests/modules/dragonflye/**
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dshbio/exportsegments:
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- modules/dshbio/exportsegments/**
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- tests/modules/dshbio/exportsegments/**
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dshbio/filterbed:
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- modules/dshbio/filterbed/**
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- tests/modules/dshbio/filterbed/**
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dshbio/filtergff3:
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- modules/dshbio/filtergff3/**
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- tests/modules/dshbio/filtergff3/**
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dshbio/splitbed:
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- modules/dshbio/splitbed/**
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- tests/modules/dshbio/splitbed/**
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dshbio/splitgff3:
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- modules/dshbio/splitgff3/**
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- tests/modules/dshbio/splitgff3/**
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ensemblvep:
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- modules/ensemblvep/**
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- tests/modules/ensemblvep/**
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expansionhunter:
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- modules/expansionhunter/**
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- tests/modules/expansionhunter/**
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fastani:
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- modules/fastani/**
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- tests/modules/fastani/**
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fastp:
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- modules/fastp/**
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- tests/modules/fastp/**
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fastqc:
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- modules/fastqc/**
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- tests/modules/fastqc/**
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fasttree:
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- modules/fasttree/**
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- tests/modules/fasttree/**
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fgbio/callmolecularconsensusreads:
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- modules/fgbio/callmolecularconsensusreads/**
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- tests/modules/fgbio/callmolecularconsensusreads/**
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fgbio/sortbam:
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- modules/fgbio/sortbam/**
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- tests/modules/fgbio/sortbam/**
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flash:
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- modules/flash/**
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- tests/modules/flash/**
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gatk4/applybqsr:
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- modules/gatk4/applybqsr/**
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- tests/modules/gatk4/applybqsr/**
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gatk4/baserecalibrator:
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- modules/gatk4/baserecalibrator/**
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- tests/modules/gatk4/baserecalibrator/**
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gatk4/bedtointervallist:
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- modules/gatk4/bedtointervallist/**
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- tests/modules/gatk4/bedtointervallist/**
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gatk4/createsequencedictionary:
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- modules/gatk4/createsequencedictionary/**
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- tests/modules/gatk4/createsequencedictionary/**
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gatk4/fastqtosam:
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- modules/gatk4/fastqtosam/**
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- tests/modules/gatk4/fastqtosam/**
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gatk4/getpileupsummaries:
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- modules/gatk4/getpileupsummaries/**
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- tests/modules/gatk4/getpileupsummaries/**
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gatk4/haplotypecaller:
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- modules/gatk4/haplotypecaller/**
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- tests/modules/gatk4/haplotypecaller/**
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gatk4/intervallisttools:
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- modules/gatk4/intervallisttools/**
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- tests/modules/gatk4/intervallisttools/**
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gatk4/markduplicates:
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- modules/gatk4/markduplicates/**
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- tests/modules/gatk4/markduplicates/**
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gatk4/mergebamalignment:
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- modules/gatk4/mergebamalignment/**
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- tests/modules/gatk4/mergebamalignment/**
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gatk4/mergevcfs:
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- modules/gatk4/mergevcfs/**
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- tests/modules/gatk4/mergevcfs/**
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gatk4/mutect2:
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- modules/gatk4/mutect2/**
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- tests/modules/gatk4/mutect2/**
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gatk4/revertsam:
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- modules/gatk4/revertsam/**
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- tests/modules/gatk4/revertsam/**
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gatk4/samtofastq:
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- modules/gatk4/samtofastq/**
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- tests/modules/gatk4/samtofastq/**
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gatk4/splitncigarreads:
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- modules/gatk4/splitncigarreads/**
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- tests/modules/gatk4/splitncigarreads/**
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gatk4/variantfiltration:
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- modules/gatk4/variantfiltration/**
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- tests/modules/gatk4/variantfiltration/**
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genmap/index:
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- modules/genmap/index/**
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- tests/modules/genmap/index/**
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genmap/mappability:
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- modules/genmap/mappability/**
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- tests/modules/genmap/mappability/**
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gffread:
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- modules/gffread/**
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- tests/modules/gffread/**
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glnexus:
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- modules/glnexus/**
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- tests/modules/glnexus/**
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graphmap2/align:
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- modules/graphmap2/align/**
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- tests/modules/graphmap2/align/**
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graphmap2/index:
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- modules/graphmap2/index/**
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- tests/modules/graphmap2/index/**
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gubbins:
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- modules/gubbins/**
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- tests/modules/gubbins/**
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gunzip:
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- modules/gunzip/**
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- tests/modules/gunzip/**
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hifiasm:
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- modules/hifiasm/**
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- tests/modules/hifiasm/**
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hisat2/align:
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- modules/hisat2/align/**
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- modules/hisat2/build/**
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- modules/hisat2/extractsplicesites/**
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- tests/modules/hisat2/align/**
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hisat2/build:
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- modules/hisat2/build/**
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- modules/hisat2/extractsplicesites/**
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- tests/modules/hisat2/build_test/**
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hisat2/extractsplicesites:
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- modules/hisat2/extractsplicesites/**
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- tests/modules/hisat2/extractsplicesites/**
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hmmer/hmmalign:
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- modules/hmmer/hmmalign/**
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- tests/modules/hmmer/hmmalign/**
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homer/annotatepeaks:
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- modules/homer/annotatepeaks/**
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- tests/modules/homer/annotatepeaks/**
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homer/findpeaks:
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- modules/homer/findpeaks/**
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- tests/modules/homer/findpeaks/**
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homer/maketagdirectory:
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- modules/homer/maketagdirectory/**
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- tests/modules/homer/maketagdirectory/**
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homer/makeucscfile:
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- modules/homer/makeucscfile/**
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- tests/modules/homer/makeucscfile/**
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iqtree:
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- modules/iqtree/**
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- tests/modules/iqtree/**
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ivar/consensus:
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- modules/ivar/consensus/**
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- tests/modules/ivar/consensus/**
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ivar/trim:
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- modules/ivar/trim/**
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- tests/modules/ivar/trim/**
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ivar/variants:
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- modules/ivar/variants/**
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- tests/modules/ivar/variants/**
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kallisto/index:
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- modules/kallisto/index/**
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- tests/modules/kallisto/index/**
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|
kallistobustools/count:
|
|
- modules/kallistobustools/count/**
|
|
- tests/modules/kallistobustools/count/**
|
|
|
|
kallistobustools/ref:
|
|
- modules/kallistobustools/ref/**
|
|
- tests/modules/kallistobustools/ref/**
|
|
|
|
kleborate:
|
|
- modules/kleborate/**
|
|
- tests/modules/kleborate/**
|
|
|
|
kraken2/kraken2:
|
|
- modules/kraken2/kraken2/**
|
|
- modules/untar/**
|
|
- tests/modules/kraken2/kraken2/**
|
|
|
|
last/dotplot:
|
|
- modules/last/dotplot/**
|
|
- tests/modules/last/dotplot/**
|
|
|
|
last/lastal:
|
|
- modules/last/lastal/**
|
|
- tests/modules/last/lastal/**
|
|
|
|
last/lastdb:
|
|
- modules/last/lastdb/**
|
|
- tests/modules/last/lastdb/**
|
|
|
|
last/mafconvert:
|
|
- modules/last/mafconvert/**
|
|
- tests/modules/last/mafconvert/**
|
|
|
|
last/mafswap:
|
|
- modules/last/mafswap/**
|
|
- tests/modules/last/mafswap/**
|
|
|
|
last/postmask:
|
|
- modules/last/postmask/**
|
|
- tests/modules/last/postmask/**
|
|
|
|
last/split:
|
|
- modules/last/split/**
|
|
- tests/modules/last/split/**
|
|
|
|
last/train:
|
|
- modules/last/train/**
|
|
- tests/modules/last/train/**
|
|
|
|
lofreq/call:
|
|
- modules/lofreq/call/**
|
|
- tests/modules/lofreq/call/**
|
|
|
|
lofreq/callparallel:
|
|
- modules/lofreq/callparallel/**
|
|
- tests/modules/lofreq/callparallel/**
|
|
|
|
lofreq/filter:
|
|
- modules/lofreq/filter/**
|
|
- tests/modules/lofreq/filter/**
|
|
|
|
lofreq/indelqual:
|
|
- modules/lofreq/indelqual/**
|
|
- tests/modules/lofreq/indelqual/**
|
|
|
|
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/**
|
|
|
|
mash/sketch:
|
|
- modules/mash/sketch/**
|
|
- tests/modules/mash/sketch/**
|
|
|
|
metaphlan3:
|
|
- modules/metaphlan3/**
|
|
- tests/modules/metaphlan3/**
|
|
|
|
methyldackel/extract:
|
|
- modules/methyldackel/extract/**
|
|
- tests/modules/methyldackel/extract/**
|
|
|
|
methyldackel/mbias:
|
|
- modules/methyldackel/mbias/**
|
|
- tests/modules/methyldackel/mbias/**
|
|
|
|
minia:
|
|
- modules/minia/**
|
|
- tests/modules/minia/**
|
|
|
|
minimap2/align:
|
|
- modules/minimap2/align/**
|
|
- tests/modules/minimap2/align/**
|
|
|
|
minimap2/index:
|
|
- modules/minimap2/index/**
|
|
- tests/modules/minimap2/index/**
|
|
|
|
mosdepth:
|
|
- modules/mosdepth/**
|
|
- tests/modules/mosdepth/**
|
|
|
|
msisensor/msi:
|
|
- modules/msisensor/msi/**
|
|
- tests/modules/msisensor/msi/**
|
|
|
|
msisensor/scan:
|
|
- modules/msisensor/scan/**
|
|
- tests/modules/msisensor/scan/**
|
|
|
|
multiqc:
|
|
- modules/fastqc/**
|
|
- modules/multiqc/**
|
|
- tests/modules/multiqc/**
|
|
|
|
muscle:
|
|
- modules/muscle/**
|
|
- tests/modules/muscle/**
|
|
|
|
nanolyse:
|
|
- modules/nanolyse/**
|
|
- tests/modules/nanolyse/**
|
|
|
|
nanoplot:
|
|
- modules/nanoplot/**
|
|
- tests/modules/nanoplot/**
|
|
|
|
nextclade:
|
|
- modules/nextclade/**
|
|
- tests/modules/nextclade/**
|
|
|
|
optitype:
|
|
- modules/optitype/**
|
|
- tests/modules/optitype/**
|
|
|
|
pairix:
|
|
- modules/pairix/**
|
|
- tests/modules/pairix/**
|
|
|
|
pairtools/dedup:
|
|
- modules/pairtools/dedup/**
|
|
- tests/modules/pairtools/dedup/**
|
|
|
|
pairtools/flip:
|
|
- modules/pairtools/flip/**
|
|
- tests/modules/pairtools/flip/**
|
|
|
|
pairtools/parse:
|
|
- modules/pairtools/parse/**
|
|
- tests/modules/pairtools/parse/**
|
|
|
|
pairtools/restrict:
|
|
- modules/pairtools/restrict/**
|
|
- tests/modules/pairtools/restrict/**
|
|
|
|
pairtools/select:
|
|
- modules/pairtools/select/**
|
|
- tests/modules/pairtools/select/**
|
|
|
|
pairtools/sort:
|
|
- modules/pairtools/sort/**
|
|
- tests/modules/pairtools/sort/**
|
|
|
|
pangolin:
|
|
- modules/pangolin/**
|
|
- tests/modules/pangolin/**
|
|
|
|
pbccs:
|
|
- modules/pbccs/**
|
|
- tests/modules/pbccs/**
|
|
|
|
picard/collectmultiplemetrics:
|
|
- modules/picard/collectmultiplemetrics/**
|
|
- tests/modules/picard/collectmultiplemetrics/**
|
|
|
|
picard/collectwgsmetrics:
|
|
- modules/picard/collectwgsmetrics/**
|
|
- tests/modules/picard/collectwgsmetrics/**
|
|
|
|
picard/filtersamreads:
|
|
- modules/picard/filtersamreads/**
|
|
- tests/modules/picard/filtersamreads/**
|
|
|
|
picard/markduplicates:
|
|
- modules/picard/markduplicates/**
|
|
- tests/modules/picard/markduplicates/**
|
|
|
|
picard/mergesamfiles:
|
|
- modules/picard/mergesamfiles/**
|
|
- tests/modules/picard/mergesamfiles/**
|
|
|
|
picard/sortsam:
|
|
- modules/picard/sortsam/**
|
|
- tests/modules/picard/sortsam/**
|
|
|
|
plasmidid:
|
|
- modules/plasmidid/**
|
|
- tests/modules/plasmidid/**
|
|
|
|
plink/vcf:
|
|
- modules/plink/vcf/**
|
|
- tests/modules/plink/vcf/**
|
|
|
|
preseq/lcextrap:
|
|
- modules/preseq/lcextrap/**
|
|
- tests/modules/preseq/lcextrap/**
|
|
|
|
prodigal:
|
|
- modules/prodigal/**
|
|
- tests/modules/prodigal/**
|
|
|
|
prokka:
|
|
- modules/prokka/**
|
|
- tests/modules/prokka/**
|
|
|
|
pycoqc:
|
|
- modules/pycoqc/**
|
|
- tests/modules/pycoqc/**
|
|
|
|
pydamage/analyze:
|
|
- modules/pydamage/analyze/**
|
|
- tests/modules/pydamage/analyze/**
|
|
|
|
pydamage/filter:
|
|
- modules/pydamage/filter/**
|
|
- tests/modules/pydamage/filter/**
|
|
|
|
qcat:
|
|
- modules/qcat/**
|
|
- tests/modules/qcat/**
|
|
|
|
qualimap/bamqc:
|
|
- modules/qualimap/bamqc/**
|
|
- tests/modules/qualimap/bamqc/**
|
|
|
|
quast:
|
|
- modules/quast/**
|
|
- tests/modules/quast/**
|
|
|
|
rapidnj:
|
|
- modules/rapidnj/**
|
|
- tests/modules/rapidnj/**
|
|
|
|
rasusa:
|
|
- modules/rasusa/**
|
|
- tests/modules/rasusa/**
|
|
|
|
raxmlng:
|
|
- modules/raxmlng/**
|
|
- tests/modules/raxmlng/**
|
|
|
|
rsem/calculateexpression:
|
|
- modules/rsem/calculateexpression/**
|
|
- tests/modules/rsem/calculateexpression/**
|
|
|
|
rsem/preparereference:
|
|
- modules/rsem/preparereference/**
|
|
- tests/modules/rsem/preparereference/**
|
|
|
|
rseqc/bamstat:
|
|
- modules/rseqc/bamstat/**
|
|
- tests/modules/rseqc/bamstat/**
|
|
|
|
rseqc/inferexperiment:
|
|
- modules/rseqc/inferexperiment/**
|
|
- tests/modules/rseqc/inferexperiment/**
|
|
|
|
rseqc/innerdistance:
|
|
- modules/rseqc/innerdistance/**
|
|
- tests/modules/rseqc/innerdistance/**
|
|
|
|
rseqc/junctionannotation:
|
|
- modules/rseqc/junctionannotation/**
|
|
- tests/modules/rseqc/junctionannotation/**
|
|
|
|
rseqc/junctionsaturation:
|
|
- modules/rseqc/junctionsaturation/**
|
|
- tests/modules/rseqc/junctionsaturation/**
|
|
|
|
rseqc/readdistribution:
|
|
- modules/rseqc/readdistribution/**
|
|
- tests/modules/rseqc/readdistribution/**
|
|
|
|
rseqc/readduplication:
|
|
- modules/rseqc/readduplication/**
|
|
- tests/modules/rseqc/readduplication/**
|
|
|
|
salmon/index:
|
|
- modules/salmon/index/**
|
|
- tests/modules/salmon/index/**
|
|
|
|
salmon/quant:
|
|
- modules/salmon/quant/**
|
|
- tests/modules/salmon/quant/**
|
|
|
|
samtools/ampliconclip:
|
|
- modules/samtools/ampliconclip/**
|
|
- tests/modules/samtools/ampliconclip/**
|
|
|
|
samtools/faidx:
|
|
- modules/samtools/faidx/**
|
|
- tests/modules/samtools/faidx/**
|
|
|
|
samtools/fastq:
|
|
- modules/samtools/fastq/**
|
|
- tests/modules/samtools/fastq/**
|
|
|
|
samtools/flagstat:
|
|
- modules/samtools/flagstat/**
|
|
- tests/modules/samtools/flagstat/**
|
|
|
|
samtools/idxstats:
|
|
- modules/samtools/idxstats/**
|
|
- tests/modules/samtools/idxstats/**
|
|
|
|
samtools/index:
|
|
- modules/samtools/index/**
|
|
- tests/modules/samtools/index/**
|
|
|
|
samtools/merge:
|
|
- modules/samtools/merge/**
|
|
- tests/modules/samtools/merge/**
|
|
|
|
samtools/mpileup:
|
|
- modules/samtools/mpileup/**
|
|
- tests/modules/samtools/mpileup/**
|
|
|
|
samtools/sort:
|
|
- modules/samtools/sort/**
|
|
- tests/modules/samtools/sort/**
|
|
|
|
samtools/stats:
|
|
- modules/samtools/stats/**
|
|
- tests/modules/samtools/stats/**
|
|
|
|
samtools/view:
|
|
- modules/samtools/view/**
|
|
- tests/modules/samtools/view/**
|
|
|
|
seacr/callpeak:
|
|
- modules/seacr/callpeak/**
|
|
- tests/modules/seacr/callpeak/**
|
|
|
|
seqkit/split2:
|
|
- modules/seqkit/split2/**
|
|
- tests/modules/seqkit/split2/**
|
|
|
|
seqtk/sample:
|
|
- modules/seqtk/sample/**
|
|
- tests/modules/seqtk/sample/**
|
|
|
|
seqtk/subseq:
|
|
- modules/seqtk/subseq/**
|
|
- tests/modules/seqtk/subseq/**
|
|
|
|
sequenzautils/bam2seqz:
|
|
- modules/sequenzautils/bam2seqz/**
|
|
- tests/modules/sequenzautils/bam2seqz/**
|
|
|
|
sequenzautils/gcwiggle:
|
|
- modules/sequenzautils/gcwiggle/**
|
|
- tests/modules/sequenzautils/gcwiggle/**
|
|
|
|
seqwish/induce:
|
|
- modules/seqwish/induce/**
|
|
- tests/modules/seqwish/induce/**
|
|
|
|
shovill:
|
|
- modules/shovill/**
|
|
- tests/modules/shovill/**
|
|
|
|
snpdists:
|
|
- modules/snpdists/**
|
|
- tests/modules/snpdists/**
|
|
|
|
snpeff:
|
|
- modules/snpeff/**
|
|
- tests/modules/snpeff/**
|
|
|
|
snpsites:
|
|
- modules/snpsites/**
|
|
- tests/modules/snpsites/**
|
|
|
|
spades:
|
|
- modules/spades/**
|
|
- tests/modules/spades/**
|
|
|
|
staphopiasccmec:
|
|
- modules/staphopiasccmec/**
|
|
- tests/modules/staphopiasccmec/**
|
|
|
|
star/align:
|
|
- modules/star/align/**
|
|
- tests/modules/star/align/**
|
|
|
|
star/genomegenerate:
|
|
- modules/star/genomegenerate/**
|
|
- tests/modules/star/genomegenerate/**
|
|
|
|
strelka/germline:
|
|
- modules/strelka/germline/**
|
|
- tests/modules/strelka/germline/**
|
|
|
|
stringtie/merge:
|
|
- modules/stringtie/merge/**
|
|
- tests/modules/stringtie/merge/**
|
|
|
|
stringtie/stringtie:
|
|
- modules/stringtie/stringtie/**
|
|
- tests/modules/stringtie/stringtie/**
|
|
|
|
subread/featurecounts:
|
|
- modules/subread/featurecounts/**
|
|
- tests/modules/subread/featurecounts/**
|
|
|
|
tabix/bgzip:
|
|
- modules/tabix/bgzip/**
|
|
- tests/modules/tabix/bgzip/**
|
|
|
|
tabix/bgziptabix:
|
|
- modules/tabix/bgziptabix/**
|
|
- tests/modules/tabix/bgziptabix/**
|
|
|
|
tabix/tabix:
|
|
- modules/tabix/tabix/**
|
|
- tests/modules/tabix/tabix/**
|
|
|
|
tiddit/sv:
|
|
- modules/tiddit/sv/**
|
|
- tests/modules/tiddit/sv/**
|
|
|
|
trimgalore:
|
|
- modules/trimgalore/**
|
|
- tests/modules/trimgalore/**
|
|
|
|
ucsc/bed12tobigbed:
|
|
- modules/ucsc/bed12tobigbed/**
|
|
- tests/modules/ucsc/bed12tobigbed/**
|
|
|
|
ucsc/bedclip:
|
|
- modules/ucsc/bedclip/**
|
|
- tests/modules/ucsc/bedclip/**
|
|
|
|
ucsc/bedgraphtobigwig:
|
|
- modules/ucsc/bedgraphtobigwig/**
|
|
- tests/modules/ucsc/bedgraphtobigwig/**
|
|
|
|
ucsc/bigwigaverageoverbed:
|
|
- modules/ucsc/bigwigaverageoverbed/**
|
|
- tests/modules/ucsc/bigwigaverageoverbed/**
|
|
|
|
ucsc/wigtobigwig:
|
|
- modules/ucsc/wigtobigwig/**
|
|
- tests/modules/ucsc/wigtobigwig/**
|
|
|
|
unicycler:
|
|
- modules/unicycler/**
|
|
- tests/modules/unicycler/**
|
|
|
|
untar:
|
|
- modules/untar/**
|
|
- tests/modules/untar/**
|
|
|
|
unzip:
|
|
- modules/unzip/**
|
|
- tests/modules/unzip/**
|
|
|
|
variantbam:
|
|
- modules/variantbam/**
|
|
- tests/modules/variantbam/**
|
|
|
|
vcftools:
|
|
- modules/vcftools/**
|
|
- tests/modules/vcftools/**
|
|
|
|
yara/index:
|
|
- modules/yara/index/**
|
|
- tests/modules/yara/index/**
|
|
|
|
yara/mapper:
|
|
- modules/yara/mapper/**
|
|
- tests/modules/yara/mapper/**
|