mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
faf77d6fee
* add nanolyse modules * add clean.fastq.gz path and md5sum * fix errors * remove unreproducible md5sum * solve linting problem * address PR suggestions * GET_NANOLYSE_FASTA as a local module * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/nanolyse/meta.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/test.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update to the version from nf-core/tools-dev * input and output files cannot have the same names * Update test.yml * Update software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update tests/software/nanolyse/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update test.yml * revert Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
652 lines
14 KiB
YAML
652 lines
14 KiB
YAML
abacas:
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- software/abacas/**
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- tests/software/abacas/**
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adapterremoval:
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- software/adapterremoval/**
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- tests/software/adapterremoval/**
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allelecounter:
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- software/allelecounter/**
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- tests/software/allelecounter/**
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artic/guppyplex:
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- software/artic/guppyplex/**
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- tests/software/artic/guppyplex/**
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bandage/image:
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- software/bandage/image/**
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- tests/software/bandage/image/**
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bcftools/consensus:
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- software/bcftools/consensus/**
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- tests/software/bcftools/consensus/**
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bcftools/filter:
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- software/bcftools/filter/**
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- tests/software/bcftools/filter/**
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bcftools/isec:
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- software/bcftools/isec/**
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- tests/software/bcftools/isec/**
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bcftools/merge:
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- software/bcftools/merge/**
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- tests/software/bcftools/merge/**
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bcftools/mpileup:
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- software/bcftools/mpileup/**
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- tests/software/bcftools/mpileup/**
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bcftools/stats:
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- software/bcftools/stats/**
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- tests/software/bcftools/stats/**
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bedtools/bamtobed:
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- software/bedtools/bamtobed/**
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- tests/software/bedtools/bamtobed/**
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bedtools/complement:
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- software/bedtools/complement/**
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- tests/software/bedtools/complement/**
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bedtools/genomecov:
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- software/bedtools/genomecov/**
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- tests/software/bedtools/genomecov/**
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bedtools/getfasta:
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- software/bedtools/getfasta/**
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- tests/software/bedtools/getfasta/**
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bedtools/intersect:
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- software/bedtools/intersect/**
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- tests/software/bedtools/intersect/**
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bedtools/maskfasta:
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- software/bedtools/maskfasta/**
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- tests/software/bedtools/maskfasta/**
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bedtools/merge:
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- software/bedtools/merge/**
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- tests/software/bedtools/merge/**
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bedtools/slop:
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- software/bedtools/slop/**
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- tests/software/bedtools/slop/**
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bedtools/sort:
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- software/bedtools/sort/**
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- tests/software/bedtools/sort/**
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bismark/align:
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- software/bismark/align/**
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- software/bismark/genomepreparation/**
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- tests/software/bismark/align/**
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bismark/deduplicate:
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- software/bismark/deduplicate/**
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- tests/software/bismark/deduplicate/**
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bismark/genomepreparation:
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- software/bismark/genomepreparation/**
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- tests/software/bismark/genomepreparation/**
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bismark/methylationextractor:
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- software/bismark/methylationextractor/**
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- software/bismark/genomepreparation/**
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- tests/software/bismark/methylationextractor/**
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bismark/report:
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- software/bismark/genomepreparation/**
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- software/bismark/align/**
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- software/bismark/deduplicate/**
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- software/bismark/methylationextractor/**
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- software/bismark/report/**
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- tests/software/bismark/report/**
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bismark/summary:
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- software/bismark/genomepreparation/**
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- software/bismark/align/**
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- software/bismark/deduplicate/**
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- software/bismark/methylationextractor/**
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- software/bismark/summary/**
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- tests/software/bismark/summary/**
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blast/blastn:
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- software/blast/blastn/**
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- tests/software/blast/blastn/**
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blast/makeblastdb:
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- software/blast/makeblastdb/**
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- tests/software/blast/makeblastdb/**
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bowtie/align:
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- software/bowtie/align/**
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- software/bowtie/build/**
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- tests/software/bowtie/align/**
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bowtie/build:
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- software/bowtie/build/**
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- tests/software/bowtie/build_test/**
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bowtie2/align:
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- software/bowtie2/align/**
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- software/bowtie2/build/**
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- tests/software/bowtie2/align/**
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bowtie2/build:
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- software/bowtie2/build/**
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- tests/software/bowtie2/build_test/**
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bwa/index:
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- software/bwa/index/**
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- tests/software/bwa/index/**
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bwa/mem:
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- software/bwa/mem/**
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- tests/software/bwa/mem/**
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bwamem2/index:
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- software/bwamem2/index/**
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- tests/software/bwamem2/index/**
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bwamem2/mem:
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- software/bwamem2/mem/**
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- tests/software/bwamem2/mem/**
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bwameth/align:
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- software/bwameth/align/**
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- tests/software/bwameth/align/**
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bwameth/index:
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- software/bwameth/index/**
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- tests/software/bwameth/index/**
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cat/fastq:
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- software/cat/fastq/**
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- tests/software/cat/fastq/**
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cnvkit:
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- software/cnvkit/**
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- tests/software/cnvkit/**
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cutadapt:
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- software/cutadapt/**
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- tests/software/cutadapt/**
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deeptools/computematrix:
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- software/deeptools/computematrix/**
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- tests/software/deeptools/computematrix/**
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deeptools/plotfingerprint:
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- software/deeptools/plotfingerprint/**
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- tests/software/deeptools/plotfingerprint/**
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deeptools/plotheatmap:
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- software/deeptools/plotheatmap/**
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- tests/software/deeptools/plotheatmap/**
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deeptools/plotprofile:
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- software/deeptools/plotprofile/**
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- tests/software/deeptools/plotprofile/**
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dshbio/filterbed:
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- software/dshbio/filterbed/**
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- tests/software/dshbio/filterbed/**
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dshbio/filtergff3:
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- software/dshbio/filtergff3/**
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- tests/software/dshbio/filtergff3/**
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dshbio/splitbed:
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- software/dshbio/splitbed/**
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- tests/software/dshbio/splitbed/**
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dshbio/splitgff3:
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- software/dshbio/splitgff3/**
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- tests/software/dshbio/splitgff3/**
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fastp:
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- software/fastp/**
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- tests/software/fastp/**
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fastqc:
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- software/fastqc/**
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- tests/software/fastqc/**
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fasttree:
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- software/fasttree/**
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- tests/software/fasttree/**
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fgbio/callmolecularconsensusreads:
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- software/fgbio/callmolecularconsensusreads/**
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- tests/software/fgbio/callmolecularconsensusreads/**
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fgbio/sortbam:
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- software/fgbio/sortbam/**
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- tests/software/fgbio/sortbam/**
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flash:
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- software/flash/**
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- tests/software/flash/**
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gatk4/applybqsr:
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- software/gatk4/applybqsr/**
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- tests/software/gatk4/applybqsr/**
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gatk4/baserecalibrator:
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- software/gatk4/baserecalibrator/**
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- tests/software/gatk4/baserecalibrator/**
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gatk4/bedtointervallist:
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- software/gatk4/bedtointervallist/**
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- tests/software/gatk4/bedtointervallist/**
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gatk4/createsequencedictionary:
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- software/gatk4/createsequencedictionary/**
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- tests/software/gatk4/createsequencedictionary/**
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gatk4/fastqtosam:
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- software/gatk4/fastqtosam/**
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- tests/software/gatk4/fastqtosam/**
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gatk4/haplotypecaller:
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- software/gatk4/haplotypecaller/**
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- tests/software/gatk4/haplotypecaller/**
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gatk4/markduplicates:
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- software/gatk4/markduplicates/**
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- tests/software/gatk4/markduplicates/**
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gatk4/mergebamalignment:
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- software/gatk4/mergebamalignment/**
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- tests/software/gatk4/mergebamalignment/**
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gatk4/mergevcfs:
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- software/gatk4/mergevcfs/**
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- tests/software/gatk4/mergevcfs/**
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gatk4/revertsam:
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- software/gatk4/revertsam/**
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- tests/software/gatk4/revertsam/**
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gatk4/samtofastq:
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- software/gatk4/samtofastq/**
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- tests/software/gatk4/samtofastq/**
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gatk4/splitncigarreads:
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- software/gatk4/splitncigarreads/**
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- tests/software/gatk4/splitncigarreads/**
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gatk4/variantfiltration:
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- software/gatk4/variantfiltration/**
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- tests/software/gatk4/variantfiltration/**
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gffread:
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- software/gffread/**
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- tests/software/gffread/**
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graphmap2/align:
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- software/graphmap2/align/**
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- tests/software/graphmap2/align/**
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graphmap2/index:
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- software/graphmap2/index/**
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- tests/software/graphmap2/index/**
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gubbins:
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- software/gubbins/**
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- tests/software/gubbins/**
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gunzip:
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- software/gunzip/**
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- tests/software/gunzip/**
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hisat2/align:
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- software/hisat2/align/**
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- software/hisat2/build/**
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- software/hisat2/extractsplicesites/**
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- tests/software/hisat2/align/**
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hisat2/build:
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- software/hisat2/build/**
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- software/hisat2/extractsplicesites/**
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- tests/software/hisat2/build_test/**
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hisat2/extractsplicesites:
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- software/hisat2/extractsplicesites/**
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- tests/software/hisat2/extractsplicesites/**
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hmmer/hmmalign:
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- software/hmmer/hmmalign/**
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- tests/software/hmmer/hmmalign/**
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homer/annotatepeaks:
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- software/homer/annotatepeaks/**
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- tests/software/homer/annotatepeaks/**
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iqtree:
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- software/iqtree/**
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- tests/software/iqtree/**
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ivar/consensus:
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- software/ivar/consensus/**
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- tests/software/ivar/consensus/**
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ivar/trim:
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- software/ivar/trim/**
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- tests/software/ivar/trim/**
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ivar/variants:
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- software/ivar/variants/**
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- tests/software/ivar/variants/**
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kallisto/index:
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- software/kallisto/index/**
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- tests/software/kallisto/index/**
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kallistobustools/count:
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- software/kallistobustools/count/**
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- tests/software/kallistobustools/count/**
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kallistobustools/ref:
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- software/kallistobustools/ref/**
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- tests/software/kallistobustools/ref/**
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kraken2/run:
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- software/kraken2/run/**
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- software/untar/**
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- tests/software/kraken2/run/**
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last/lastdb:
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- software/last/lastdb/**
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- tests/software/last/lastdb/**
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mash/sketch:
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- software/mash/sketch/**
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- tests/software/mash/sketch/**
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methyldackel/extract:
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- software/methyldackel/extract/**
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- tests/software/methyldackel/extract/**
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methyldackel/mbias:
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- software/methyldackel/mbias/**
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- tests/software/methyldackel/mbias/**
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minia:
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- software/minia/**
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- tests/software/minia/**
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minimap2/align:
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- software/minimap2/align/**
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- tests/software/minimap2/align/**
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minimap2/index:
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- software/minimap2/index/**
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- tests/software/minimap2/index/**
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mosdepth:
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- software/mosdepth/**
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- tests/software/mosdepth/**
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msisensor/msi:
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- software/msisensor/msi/**
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- tests/software/msisensor/msi/**
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msisensor/scan:
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- software/msisensor/scan/**
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- tests/software/msisensor/scan/**
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multiqc:
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- software/fastqc/**
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- software/multiqc/**
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- tests/software/multiqc/**
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nanolyse:
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- software/nanolyse/**
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- tests/software/nanolyse/**
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nanoplot:
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- software/nanoplot/**
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- tests/software/nanoplot/**
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optitype:
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- software/optitype/**
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- tests/software/optitype/**
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pangolin:
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- software/pangolin/**
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- tests/software/pangolin/**
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picard/collectmultiplemetrics:
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- software/picard/collectmultiplemetrics/**
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- tests/software/picard/collectmultiplemetrics/**
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picard/collectwgsmetrics:
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- software/picard/collectwgsmetrics/**
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- tests/software/picard/collectwgsmetrics/**
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picard/markduplicates:
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- software/picard/markduplicates/**
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- tests/software/picard/markduplicates/**
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picard/mergesamfiles:
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- software/picard/mergesamfiles/**
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- tests/software/picard/mergesamfiles/**
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plasmidid:
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- software/plasmidid/**
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- tests/software/plasmidid/**
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preseq/lcextrap:
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- software/preseq/lcextrap/**
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- tests/software/preseq/lcextrap/**
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prodigal:
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- software/prodigal/**
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- tests/software/prodigal/**
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prokka:
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- software/prokka/**
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- tests/software/prokka/**
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pycoqc:
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- software/pycoqc/**
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- tests/software/pycoqc/**
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qcat:
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- software/qcat/**
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- tests/software/qcat/**
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qualimap/bamqc:
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- software/qualimap/bamqc/**
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- tests/software/qualimap/bamqc/**
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quast:
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- software/quast/**
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- tests/software/quast/**
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rapidnj:
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- software/rapidnj/**
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- tests/software/rapidnj/**
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rasusa:
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- software/rasusa/**
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- tests/software/rasusa/**
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raxmlng:
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- software/raxmlng/**
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- tests/software/raxmlng/**
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rseqc/bamstat:
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- software/rseqc/bamstat/**
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- tests/software/rseqc/bamstat/**
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rseqc/inferexperiment:
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- software/rseqc/inferexperiment/**
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- tests/software/rseqc/inferexperiment/**
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rseqc/innerdistance:
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- software/rseqc/innerdistance/**
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- tests/software/rseqc/innerdistance/**
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rseqc/readdistribution:
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- software/rseqc/readdistribution/**
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- tests/software/rseqc/readdistribution/**
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rseqc/readduplication:
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- software/rseqc/readduplication/**
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- tests/software/rseqc/readduplication/**
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salmon/index:
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- software/salmon/index/**
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- tests/software/salmon/index/**
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salmon/quant:
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- software/salmon/quant/**
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- tests/software/salmon/quant/**
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samtools/faidx:
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- software/samtools/faidx/**
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- tests/software/samtools/faidx/**
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samtools/fastq:
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- software/samtools/fastq/**
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- tests/software/samtools/fastq/**
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samtools/flagstat:
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- software/samtools/flagstat/**
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- tests/software/samtools/flagstat/**
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samtools/idxstats:
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- software/samtools/idxstats/**
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|
- tests/software/samtools/idxstats/**
|
|
|
|
samtools/index:
|
|
- software/samtools/index/**
|
|
- tests/software/samtools/index/**
|
|
|
|
samtools/merge:
|
|
- software/samtools/merge/**
|
|
- tests/software/samtools/merge/**
|
|
|
|
samtools/mpileup:
|
|
- software/samtools/mpileup/**
|
|
- tests/software/samtools/mpileup/**
|
|
|
|
samtools/sort:
|
|
- software/samtools/sort/**
|
|
- tests/software/samtools/sort/**
|
|
|
|
samtools/stats:
|
|
- software/samtools/stats/**
|
|
- tests/software/samtools/stats/**
|
|
|
|
samtools/view:
|
|
- software/samtools/view/**
|
|
- tests/software/samtools/view/**
|
|
|
|
seacr/callpeak:
|
|
- software/seacr/callpeak/**
|
|
- tests/software/seacr/callpeak/**
|
|
|
|
seqkit/split2:
|
|
- software/seqkit/split2/**
|
|
- tests/software/seqkit/split2/**
|
|
|
|
sequenzautils/bam2seqz:
|
|
- software/sequenzautils/bam2seqz/**
|
|
- tests/software/sequenzautils/bam2seqz/**
|
|
|
|
sequenzautils/gcwiggle:
|
|
- software/sequenzautils/gcwiggle/**
|
|
- tests/software/sequenzautils/gcwiggle/**
|
|
|
|
seqwish/induce:
|
|
- software/seqwish/induce/**
|
|
- tests/software/seqwish/induce/**
|
|
|
|
shovill:
|
|
- software/shovill/**
|
|
- tests/software/shovill/**
|
|
|
|
snpsites:
|
|
- software/snpsites/**
|
|
- tests/software/snpsites/**
|
|
|
|
spades:
|
|
- software/spades/**
|
|
- tests/software/spades/**
|
|
|
|
star/align:
|
|
- software/star/align/**
|
|
- tests/software/star/align/**
|
|
|
|
star/genomegenerate:
|
|
- software/star/genomegenerate/**
|
|
- tests/software/star/genomegenerate/**
|
|
|
|
strelka/germline:
|
|
- software/strelka/germline/**
|
|
- tests/software/strelka/germline/**
|
|
|
|
stringtie/merge:
|
|
- software/stringtie/merge/**
|
|
- tests/software/stringtie/merge/**
|
|
|
|
stringtie/stringtie:
|
|
- software/stringtie/stringtie/**
|
|
- tests/software/stringtie/stringtie/**
|
|
|
|
subread/featurecounts:
|
|
- software/subread/featurecounts/**
|
|
- tests/software/subread/featurecounts/**
|
|
|
|
tabix/bgzip:
|
|
- software/tabix/bgzip/**
|
|
- tests/software/tabix/bgzip/**
|
|
|
|
tabix/tabix:
|
|
- software/tabix/tabix/**
|
|
- tests/software/tabix/tabix/**
|
|
|
|
tiddit/sv:
|
|
- software/tiddit/sv/**
|
|
- tests/software/tiddit/sv/**
|
|
|
|
trimgalore:
|
|
- software/trimgalore/**
|
|
- tests/software/trimgalore/**
|
|
|
|
ucsc/bed12tobigbed:
|
|
- software/ucsc/bed12tobigbed/**
|
|
- tests/software/ucsc/bed12tobigbed/**
|
|
|
|
ucsc/bedclip:
|
|
- software/ucsc/bedclip/**
|
|
- tests/software/ucsc/bedclip/**
|
|
|
|
ucsc/bedgraphtobigwig:
|
|
- software/ucsc/bedgraphtobigwig/**
|
|
- tests/software/ucsc/bedgraphtobigwig/**
|
|
|
|
unicycler:
|
|
- software/unicycler/**
|
|
- tests/software/unicycler/**
|
|
|
|
untar:
|
|
- software/untar/**
|
|
- tests/software/untar/**
|
|
|
|
vcftools:
|
|
- software/vcftools/**
|
|
- tests/software/vcftools/**
|
|
|
|
yara/index:
|
|
- software/yara/index/**
|
|
- tests/software/yara/index/**
|
|
|
|
yara/mapper:
|
|
- software/yara/mapper/**
|
|
- tests/software/yara/mapper/**
|