mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
Lint modules ci (#389)
* ci: Add modules lint step Moved it ahead of the nextflow install so ideally it'll fail before we bother doing any more setup * ci: _ => / * Update tests/config/pytest_software.yml Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
Edmund Miller
GitHub
parent
710ab76b90
commit
a3684d9594
88 changed files with 233 additions and 225 deletions
20
.github/workflows/pytest-workflow.yml
vendored
20
.github/workflows/pytest-workflow.yml
vendored
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@ -40,6 +40,20 @@ jobs:
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key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# FIXME: Remove this when nf-core modules lint stabilizes
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- name: Install nf-core tools development version
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run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev
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- name: Lint ${{ matrix.tags }}
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run: nf-core modules lint . -t ${{ matrix.tags }}
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- uses: actions/cache@v2
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with:
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path: /usr/local/bin/nextflow
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@ -54,12 +68,6 @@ jobs:
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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- name: Set up Singularity
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if: matrix.profile == 'singularity'
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@ -6,85 +6,85 @@ allelecounter:
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- software/allelecounter/**
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- tests/software/allelecounter/**
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bandage_image:
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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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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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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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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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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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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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bcftools/stats:
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- software/bcftools/stats/**
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- tests/software/bcftools/stats/**
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bedtools_complement:
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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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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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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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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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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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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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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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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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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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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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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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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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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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@ -92,7 +92,7 @@ bismark_report:
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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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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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@ -100,57 +100,57 @@ bismark_summary:
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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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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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blast/makeblastdb:
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- software/blast/makeblastdb/**
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- tests/software/blast/makeblastdb/**
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bowtie2_align:
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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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bowtie2/build:
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- software/bowtie2/build/**
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- tests/software/bowtie2/build_test/**
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bowtie_align:
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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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bowtie/build:
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- software/bowtie/build/**
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- tests/software/bowtie/build_test/**
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bwa_index:
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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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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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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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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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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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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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cat/fastq:
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- software/cat/fastq/**
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- tests/software/cat/fastq/**
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@ -162,11 +162,11 @@ cutadapt:
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- software/cutadapt/**
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- tests/software/cutadapt/**
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dsh_filterbed:
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dsh/filterbed:
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- software/dsh/filterbed/**
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- tests/software/dsh/filterbed/**
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dsh_splitbed:
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dsh/splitbed:
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- software/dsh/splitbed/**
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- tests/software/dsh/splitbed/**
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@ -190,55 +190,55 @@ flash:
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- software/flash/**
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- tests/software/flash/**
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gatk4_applybqsr:
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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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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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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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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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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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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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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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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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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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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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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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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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gatk4/variantfiltration:
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- software/gatk4/variantfiltration/**
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- tests/software/gatk4/variantfiltration/**
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@ -254,50 +254,50 @@ gunzip:
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- software/gunzip/**
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- tests/software/gunzip/**
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hisat2_align:
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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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|
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hisat2_build:
|
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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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hisat2/extractsplicesites:
|
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- software/hisat2/extractsplicesites/**
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- tests/software/hisat2/extractsplicesites/**
|
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|
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homer_annotatepeaks:
|
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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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|
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ivar_consensus:
|
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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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|
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ivar_trim:
|
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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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|
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ivar_variants:
|
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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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|
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kallisto_index:
|
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kallisto/index:
|
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- software/kallisto/index/**
|
||||
- tests/software/kallisto/index/**
|
||||
|
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kraken2_run:
|
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kraken2/run:
|
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- software/kraken2/run/**
|
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- tests/software/kraken2/run/**
|
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|
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methyldackel_extract:
|
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methyldackel/extract:
|
||||
- software/methyldackel/extract/**
|
||||
- tests/software/methyldackel/extract/**
|
||||
|
||||
methyldackel_mbias:
|
||||
methyldackel/mbias:
|
||||
- software/methyldackel/mbias/**
|
||||
- tests/software/methyldackel/mbias/**
|
||||
|
||||
|
|
@ -305,7 +305,7 @@ minia:
|
|||
- software/minia/**
|
||||
- tests/software/minia/**
|
||||
|
||||
minimap2_align:
|
||||
minimap2/align:
|
||||
- software/minimap2/align/**
|
||||
- tests/software/minimap2/align/**
|
||||
|
||||
|
|
@ -334,23 +334,23 @@ pangolin:
|
|||
- software/pangolin/**
|
||||
- tests/software/pangolin/**
|
||||
|
||||
picard_collectmultiplemetrics:
|
||||
picard/collectmultiplemetrics:
|
||||
- software/picard/collectmultiplemetrics/**
|
||||
- tests/software/picard/collectmultiplemetrics/**
|
||||
|
||||
picard_collectwgsmetrics:
|
||||
picard/collectwgsmetrics:
|
||||
- software/picard/collectwgsmetrics/**
|
||||
- tests/software/picard/collectwgsmetrics/**
|
||||
|
||||
picard_markduplicates:
|
||||
picard/markduplicates:
|
||||
- software/picard/markduplicates/**
|
||||
- tests/software/picard/markduplicates/**
|
||||
|
||||
picard_mergesamfiles:
|
||||
picard/mergesamfiles:
|
||||
- software/picard/mergesamfiles/**
|
||||
- tests/software/picard/mergesamfiles/**
|
||||
|
||||
preseq_lcextrap:
|
||||
preseq/lcextrap:
|
||||
- software/preseq/lcextrap/**
|
||||
- tests/software/preseq/lcextrap/**
|
||||
|
||||
|
|
@ -362,7 +362,7 @@ prokka:
|
|||
- software/prokka/**
|
||||
- tests/software/prokka/**
|
||||
|
||||
qualimap_bamqc:
|
||||
qualimap/bamqc:
|
||||
- software/qualimap/bamqc/**
|
||||
- tests/software/qualimap/bamqc/**
|
||||
|
||||
|
|
@ -370,79 +370,79 @@ quast:
|
|||
- software/quast/**
|
||||
- tests/software/quast/**
|
||||
|
||||
salmon_index:
|
||||
salmon/index:
|
||||
- software/salmon/index/**
|
||||
- tests/software/salmon/index/**
|
||||
|
||||
salmon_quant:
|
||||
salmon/quant:
|
||||
- software/salmon/quant/**
|
||||
- tests/software/salmon/quant/**
|
||||
|
||||
samtools_faidx:
|
||||
samtools/faidx:
|
||||
- software/samtools/faidx/**
|
||||
- tests/software/samtools/faidx/**
|
||||
|
||||
samtools_fastq:
|
||||
samtools/fastq:
|
||||
- software/samtools/fastq/**
|
||||
- tests/software/samtools/fastq/**
|
||||
|
||||
samtools_flagstat:
|
||||
samtools/flagstat:
|
||||
- software/samtools/flagstat/**
|
||||
- tests/software/samtools/flagstat/**
|
||||
|
||||
samtools_idxstats:
|
||||
samtools/idxstats:
|
||||
- software/samtools/idxstats/**
|
||||
- tests/software/samtools/idxstats/**
|
||||
|
||||
samtools_index:
|
||||
samtools/index:
|
||||
- software/samtools/index/**
|
||||
- tests/software/samtools/index/**
|
||||
|
||||
samtools_merge:
|
||||
samtools/merge:
|
||||
- software/samtools/merge/**
|
||||
- tests/software/samtools/merge/**
|
||||
|
||||
samtools_mpileup:
|
||||
samtools/mpileup:
|
||||
- software/samtools/mpileup/**
|
||||
- tests/software/samtools/mpileup/**
|
||||
|
||||
samtools_sort:
|
||||
samtools/sort:
|
||||
- software/samtools/sort/**
|
||||
- tests/software/samtools/sort/**
|
||||
|
||||
samtools_stats:
|
||||
samtools/stats:
|
||||
- software/samtools/stats/**
|
||||
- tests/software/samtools/stats/**
|
||||
|
||||
samtools_view:
|
||||
samtools/view:
|
||||
- software/samtools/view/**
|
||||
- tests/software/samtools/view/**
|
||||
|
||||
seacr_callpeak:
|
||||
seacr/callpeak:
|
||||
- software/seacr/callpeak/**
|
||||
- tests/software/seacr/callpeak/**
|
||||
|
||||
seqkit_split2:
|
||||
seqkit/split2:
|
||||
- software/seqkit/split2/**
|
||||
- tests/software/seqkit/split2/**
|
||||
|
||||
sequenza_bam2seqz:
|
||||
sequenza/bam2seqz:
|
||||
- software/sequenza/bam2seqz/**
|
||||
- tests/software/sequenza/bam2seqz/**
|
||||
|
||||
sequenza_wiggle:
|
||||
sequenza/wiggle:
|
||||
- software/sequenza/wiggle/**
|
||||
- tests/software/sequenza/wiggle/**
|
||||
|
||||
sequenzautils_bam2seqz:
|
||||
sequenzautils/bam2seqz:
|
||||
- software/sequenzautils/bam2seqz/**
|
||||
- tests/software/sequenzautils/bam2seqz/**
|
||||
|
||||
sequenzautils_gcwiggle:
|
||||
sequenzautils/gcwiggle:
|
||||
- software/sequenzautils/gcwiggle/**
|
||||
- tests/software/sequenzautils/gcwiggle/**
|
||||
|
||||
seqwish_induce:
|
||||
seqwish/induce:
|
||||
- software/seqwish/induce/**
|
||||
- tests/software/seqwish/induce/**
|
||||
|
||||
|
|
@ -454,15 +454,15 @@ spades:
|
|||
- software/spades/**
|
||||
- tests/software/spades/**
|
||||
|
||||
star_align:
|
||||
star/align:
|
||||
- software/star/align/**
|
||||
- tests/software/star/align/**
|
||||
|
||||
star_genomegenerate:
|
||||
star/genomegenerate:
|
||||
- software/star/genomegenerate/**
|
||||
- tests/software/star/genomegenerate/**
|
||||
|
||||
strelka_germline:
|
||||
strelka/germline:
|
||||
- software/strelka/germline/**
|
||||
- tests/software/strelka/germline/**
|
||||
|
||||
|
|
@ -470,19 +470,19 @@ stringtie:
|
|||
- software/stringtie/**
|
||||
- tests/software/stringtie/**
|
||||
|
||||
subread_featurecounts:
|
||||
subread/featurecounts:
|
||||
- software/subread/featurecounts/**
|
||||
- tests/software/subread/featurecounts/**
|
||||
|
||||
tabix_bgzip:
|
||||
tabix/bgzip:
|
||||
- software/tabix/bgzip/**
|
||||
- tests/software/tabix/bgzip/**
|
||||
|
||||
tabix_tabix:
|
||||
tabix/tabix:
|
||||
- software/tabix/tabix/**
|
||||
- tests/software/tabix/tabix/**
|
||||
|
||||
tiddit_sv:
|
||||
tiddit/sv:
|
||||
- software/tiddit/sv/**
|
||||
- tests/software/tiddit/sv/**
|
||||
|
||||
|
|
@ -490,11 +490,11 @@ trimgalore:
|
|||
- software/trimgalore/**
|
||||
- tests/software/trimgalore/**
|
||||
|
||||
ucsc_bed12tobigbed:
|
||||
ucsc/bed12tobigbed:
|
||||
- software/ucsc/bed12tobigbed/**
|
||||
- tests/software/ucsc/bed12tobigbed/**
|
||||
|
||||
ucsc_bedgraphtobigwig:
|
||||
ucsc/bedgraphtobigwig:
|
||||
- software/ucsc/bedgraphtobigwig/**
|
||||
- tests/software/ucsc/bedgraphtobigwig/**
|
||||
|
||||
|
|
@ -514,6 +514,6 @@ yara:
|
|||
- software/yara/mapper/**
|
||||
- tests/software/yara/mapper/**
|
||||
|
||||
yara_index:
|
||||
yara/index:
|
||||
- software/yara/index/**
|
||||
- tests/software/yara/index/**
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bandage/image -entry test_bandage_image -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bandage
|
||||
- bandage_image
|
||||
- bandage/image
|
||||
files:
|
||||
- path: output/bandage/B-3106.png
|
||||
- path: output/bandage/B-3106.svg
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: bcftools consensus test_bcftools_consensus
|
||||
command: nextflow run tests/software/bcftools/consensus -entry test_bcftools_consensus -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bcftools_consensus
|
||||
- bcftools/consensus
|
||||
- bcftools
|
||||
files:
|
||||
- path: output/bcftools/test.fa
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: bcftools filter test_bcftools_filter
|
||||
command: nextflow run tests/software/bcftools/filter -entry test_bcftools_filter -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bcftools_filter
|
||||
- bcftools/filter
|
||||
- bcftools
|
||||
files:
|
||||
- path: output/bcftools/test.vcf.gz
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/bcftools/isec -entry test_bcftools_isec -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bcftools
|
||||
- bcftools_isec
|
||||
- bcftools/isec
|
||||
files:
|
||||
- path: output/bcftools/test/0000.vcf.gz
|
||||
md5sum: fc178eb342a91dc0d1d568601ad8f8e2
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: bcftools merge test_bcftools_merge
|
||||
command: nextflow run tests/software/bcftools/merge -entry test_bcftools_merge -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bcftools_merge
|
||||
- bcftools/merge
|
||||
- bcftools
|
||||
files:
|
||||
- path: output/bcftools/test.vcf.gz
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: bcftools mpileup test_bcftools_mpileup
|
||||
command: nextflow run tests/software/bcftools/mpileup -entry test_bcftools_mpileup -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bcftools_mpileup
|
||||
- bcftools/mpileup
|
||||
- bcftools
|
||||
files:
|
||||
- path: output/bcftools/test.bcftools_stats.txt
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/bcftools/stats -entry test_bcftools_stats -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bcftools
|
||||
- bcftools_stats
|
||||
- bcftools/stats
|
||||
files:
|
||||
- path: output/bcftools/test.bcftools_stats.txt
|
||||
md5sum: c4c5938add12a20050eec3782c8ad623
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bedtools/complement -entry test_bedtools_complement -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools_complement
|
||||
- bedtools/complement
|
||||
files:
|
||||
- path: ./output/bedtools/test_out.bed
|
||||
md5sum: d71df7e47aec0661c27b71e483e727f9
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bedtools/genomecov -entry test_bedtools_genomecov -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools_genomecov
|
||||
- bedtools/genomecov
|
||||
files:
|
||||
- path: ./output/bedtools/test_out.bed
|
||||
md5sum: 66083198daca6c001d328ba9616e9b53
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bedtools/getfasta -entry test_bedtools_getfasta -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools_getfasta
|
||||
- bedtools/getfasta
|
||||
files:
|
||||
- path: ./output/bedtools/test.fa
|
||||
md5sum: 41c3a45a57a16c04f828d8f8bb52df70
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bedtools/intersect -entry test_bedtools_intersect -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools_intersect
|
||||
- bedtools/intersect
|
||||
files:
|
||||
- path: ./output/bedtools/test_out.bed
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bedtools/maskfasta -entry test_bedtools_maskfasta -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools_maskfasta
|
||||
- bedtools/maskfasta
|
||||
files:
|
||||
- path: ./output/bedtools/test.fa
|
||||
md5sum: f4f6749698f11074228d2c79338e3b9c
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bedtools/merge -entry test_bedtools_merge -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools_merge
|
||||
- bedtools/merge
|
||||
files:
|
||||
- path: ./output/bedtools/test_out.bed
|
||||
md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bedtools/slop -entry test_bedtools_slop -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools_slop
|
||||
- bedtools/slop
|
||||
files:
|
||||
- path: ./output/bedtools/test_out.bed
|
||||
md5sum: 4f1d8924925fe5d205c9e1981fe290a4
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bedtools/sort -entry test_bedtools_sort -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bedtools
|
||||
- bedtools_sort
|
||||
- bedtools/sort
|
||||
files:
|
||||
- path: ./output/bedtools/test_out.bed
|
||||
md5sum: fe4053cf4de3aebbdfc3be2efb125a74
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
- bismark_align
|
||||
- bismark/align
|
||||
files:
|
||||
- path: output/test_single_end/test_methylated_1_bismark_bt2.bam
|
||||
md5sum: 7f9744cec5aa7908675e5fae79af36fc
|
||||
|
|
@ -12,7 +12,7 @@
|
|||
command: nextflow run ./tests/software/bismark/align -entry test_bismark_align_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
- bismark_align
|
||||
- bismark/align
|
||||
files:
|
||||
- path: output/test_paired_end/test_methylated_1_bismark_bt2_pe.bam
|
||||
md5sum: b13d0d40dffd336375f80fc94acc295f
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bismark/deduplicate -entry test_bismark_deduplicate -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
- bismark_deduplicate
|
||||
- bismark/deduplicate
|
||||
files:
|
||||
- path: output/bismark/test_methylated_paired_end.deduplicated.bam
|
||||
- path: output/bismark/test_methylated_paired_end.deduplication_report.txt
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bismark/genomepreparation -entry test_bismark_genomepreparation -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
- bismark_genomepreparation
|
||||
- bismark/genomepreparation
|
||||
files:
|
||||
- path: ./output/bismark/BismarkIndex/genome.fasta
|
||||
md5sum: 6e9fe4042a72f2345f644f239272b7e6
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bismark/methylationextractor -entry test_bismark_methylationextractor -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
- bismark_methylationextractor
|
||||
- bismark/methylationextractor
|
||||
files:
|
||||
- path: output/bismark/CHG_OB_test_methylated_paired_end.txt.gz
|
||||
- path: output/bismark/CHG_OT_test_methylated_paired_end.txt.gz
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bismark/report -entry test_bismark_report -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
- bismark_report
|
||||
- bismark/report
|
||||
files:
|
||||
- path: output/bismark/test_methylated_1_bismark_bt2_PE_report.txt
|
||||
- path: output/bismark/test_methylated_1_bismark_bt2_PE_report.html
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bismark/summary -entry test_bismark_summary -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bismark
|
||||
- bismark_summary
|
||||
- bismark/summary
|
||||
files:
|
||||
- path: output/bismark/bismark_summary_report.html
|
||||
- path: output/bismark/bismark_summary_report.txt
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/blast/blastn -entry test_blast_blastn -c tests/config/nextflow.config
|
||||
tags:
|
||||
- blast
|
||||
- blast_blastn
|
||||
- blast/blastn
|
||||
files:
|
||||
- path: ./output/blast/test.blastn.txt
|
||||
- path: ./output/blast/blast_db/genome.fasta.nsq
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/blast/makeblastdb -entry test_blast_makeblastdb -c tests/config/nextflow.config
|
||||
tags:
|
||||
- blast
|
||||
- blast_makeblastdb
|
||||
- blast/makeblastdb
|
||||
files:
|
||||
- path: ./output/blast/blast_db/genome.fasta.nsq
|
||||
md5sum: 982cbc7d9e38743b9b1037588862b9da
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_align_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bowtie
|
||||
- bowtie_align
|
||||
- bowtie/align
|
||||
- bowtie_align_single_end
|
||||
files:
|
||||
- path: ./output/bowtie/test.bam
|
||||
|
|
@ -25,7 +25,7 @@
|
|||
command: nextflow run ./tests/software/bowtie/align -entry test_bowtie_align_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bowtie
|
||||
- bowtie_align
|
||||
- bowtie/align
|
||||
- bowtie_align_paired_end
|
||||
files:
|
||||
- path: ./output/bowtie/test.bam
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bowtie/build_test -entry test_bowtie_build -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bowtie
|
||||
- bowtie_build
|
||||
- bowtie/build
|
||||
files:
|
||||
- path: ./output/index/bowtie/test_genome.3.ebwt
|
||||
md5sum: 4ed93abba181d8dfab2e303e33114777
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bowtie2
|
||||
- bowtie2_align
|
||||
- bowtie2/align
|
||||
- bowtie2_align_single_end
|
||||
files:
|
||||
- path: ./output/bowtie2/test.bam
|
||||
|
|
@ -24,7 +24,7 @@
|
|||
command: nextflow run ./tests/software/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bowtie2
|
||||
- bowtie2_align
|
||||
- bowtie2/align
|
||||
- bowtie2_align_paired_end
|
||||
files:
|
||||
- path: ./output/bowtie2/test.bam
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bowtie2/build_test -entry test_bowtie2_build -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bowtie2
|
||||
- bowtie2_build
|
||||
- bowtie2/build
|
||||
files:
|
||||
- path: ./output/index/bowtie2/genome.3.bt2
|
||||
md5sum: 4ed93abba181d8dfab2e303e33114777
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bwa/index -entry test_bwa_index -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwa
|
||||
- bwa_index
|
||||
- bwa/index
|
||||
files:
|
||||
- path: ./output/index/bwa/genome.bwt
|
||||
md5sum: 0469c30a1e239dd08f68afe66fde99da
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwa
|
||||
- bwa_mem
|
||||
- bwa/mem
|
||||
- bwa_mem_single_end
|
||||
files:
|
||||
- path: ./output/bwa/test.bam
|
||||
|
|
@ -22,7 +22,7 @@
|
|||
command: nextflow run ./tests/software/bwa/mem -entry test_bwa_mem_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwa
|
||||
- bwa_mem
|
||||
- bwa/mem
|
||||
- bwa_mem_paired_end
|
||||
files:
|
||||
- path: ./output/bwa/test.bam
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bwamem2/index -entry test_bwamem2_index -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwamem2
|
||||
- bwamem2_index
|
||||
- bwamem2/index
|
||||
files:
|
||||
- path: ./output/index/bwamem2/genome.fasta.amb
|
||||
md5sum: 3a68b8b2287e07dd3f5f95f4344ba76e
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bwamem2/mem -entry test_bwamem2_mem_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwamem2
|
||||
- bwamem2_mem
|
||||
- bwamem2/mem
|
||||
- bwamem2_mem_single_end
|
||||
files:
|
||||
- path: ./output/bwamem2/test.bam
|
||||
|
|
@ -22,7 +22,7 @@
|
|||
command: nextflow run ./tests/software/bwamem2/mem -entry test_bwamem2_mem_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwamem2
|
||||
- bwamem2_mem
|
||||
- bwamem2/mem
|
||||
- bwamem2_mem_paired_end
|
||||
files:
|
||||
- path: ./output/bwamem2/test.bam
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bwameth/align -entry test_bwameth_align_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwameth
|
||||
- bwameth_align
|
||||
- bwameth/align
|
||||
files:
|
||||
- path: output/test_single_end/test.bam
|
||||
|
||||
|
|
@ -10,7 +10,7 @@
|
|||
command: nextflow run ./tests/software/bwameth/align -entry test_bwameth_align_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwameth
|
||||
- bwameth_align
|
||||
- bwameth/align
|
||||
files:
|
||||
- path: output/test_paired_end/test.bam
|
||||
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/bwameth/index -entry test_bwameth_index -c tests/config/nextflow.config
|
||||
tags:
|
||||
- bwameth
|
||||
- bwameth_index
|
||||
- bwameth/index
|
||||
files:
|
||||
- path: ./output/index/bwameth/genome.fasta.bwameth.c2t
|
||||
md5sum: 98039984526a41d04d6bd92fcc040c62
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/cat/fastq -entry test_cat_fastq_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- cat
|
||||
- cat_fastq
|
||||
- cat/fastq
|
||||
- cat_fastqc_single_end
|
||||
files:
|
||||
- path: ./output/merged_fastq/test.merged.fastq.gz
|
||||
|
|
@ -12,7 +12,7 @@
|
|||
command: nextflow run ./tests/software/cat/fastq -entry test_cat_fastq_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- cat
|
||||
- cat_fastq
|
||||
- cat/fastq
|
||||
- cat_fastqc_paired_end
|
||||
files:
|
||||
- path: ./output/merged_fastq/test_2.merged.fastq.gz
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/dsh/filterbed -entry test_dsh_filterbed -c tests/config/nextflow.config
|
||||
tags:
|
||||
- dsh
|
||||
- dsh_filterbed
|
||||
- dsh/filterbed
|
||||
files:
|
||||
- path: ./output/dsh/test.filtered.bed.gz
|
||||
md5sum: 163be0a88c70ca629fd516dbaadad96a
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/dsh/splitbed -entry test_dsh_splitbed -c tests/config/nextflow.config
|
||||
tags:
|
||||
- dsh
|
||||
- dsh_splitbed
|
||||
- dsh/splitbed
|
||||
files:
|
||||
- path: ./output/dsh/test.1.bed.gz
|
||||
md5sum: 967ba338f361740eb015304003ababe7
|
||||
|
|
|
|||
|
|
@ -1,8 +1,8 @@
|
|||
- name: gatk4 applybqsr test_gatk4_applybqsr
|
||||
command: nextflow run tests/software/gatk4/applybqsr -entry test_gatk4_applybqsr -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4_applybqsr
|
||||
- gatk4
|
||||
- gatk4/applybqsr
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 139a5ffc7601ce3cfa7a896cd381542a
|
||||
|
|
@ -10,9 +10,9 @@
|
|||
- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
|
||||
command: nextflow run tests/software/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4_applybqsr
|
||||
- gatk4_applybqsr_intervals
|
||||
- gatk4
|
||||
- gatk4/applybqsr/intervals
|
||||
- gatk4/applybqsr
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 5b1f6fa2525124c281f71e5a76d28482
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator
|
||||
command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4_baserecalibrator
|
||||
- gatk4/baserecalibrator
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.table
|
||||
|
|
@ -10,8 +10,8 @@
|
|||
- name: gatk4 baserecalibrator test_gatk4_baserecalibrator_intervals
|
||||
command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_intervals -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4_baserecalibrator_intervals
|
||||
- gatk4_baserecalibrator
|
||||
- gatk4/baserecalibrator/intervals
|
||||
- gatk4/baserecalibrator
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.table
|
||||
|
|
@ -21,7 +21,7 @@
|
|||
command: nextflow run tests/software/gatk4/baserecalibrator -entry test_gatk4_baserecalibrator_multiple_sites -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4_baserecalibrator_multiple_sites
|
||||
- gatk4_baserecalibrator
|
||||
- gatk4/baserecalibrator
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.table
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/gatk4/bedtointervallist -entry test_gatk4_bedtointervallist -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4_bedtointervallist
|
||||
- gatk4/bedtointervallist
|
||||
files:
|
||||
- path: output/gatk4/test.interval_list
|
||||
md5sum: e51101c9357fb2d59fd30e370eefa39c
|
||||
|
|
|
|||
|
|
@ -2,8 +2,8 @@
|
|||
command: nextflow run tests/software/gatk4/fastqtosam -entry test_gatk4_fastqtosam_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4_fastqtosam_single_end
|
||||
- gatk4/fastqtosam
|
||||
- gatk4
|
||||
- gatk4_fastqtosam
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 4967100b2e4912c0e4ce0976d946bafb
|
||||
|
|
@ -13,7 +13,7 @@
|
|||
tags:
|
||||
- gatk4_fastqtosam_paired_end
|
||||
- gatk4
|
||||
- gatk4_fastqtosam
|
||||
- gatk4/fastqtosam
|
||||
files:
|
||||
- path: output/gatk4/test.bam
|
||||
md5sum: 4967100b2e4912c0e4ce0976d946bafb
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4_mergebamalignment
|
||||
- gatk4/mergebamalignment
|
||||
files:
|
||||
- path: output/gatk4/test.merged.bam
|
||||
md5sum: bd4a5e2ea916826aadebb5878333e26f
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: gatk4 mergevcfs test_gatk4_mergevcfs
|
||||
command: nextflow run tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4_mergevcfs
|
||||
- gatk4/mergevcfs
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.merged.vcf.gz
|
||||
|
|
@ -10,9 +10,9 @@
|
|||
- name: gatk4 mergevcfs test_gatk4_mergevcfs_refdict
|
||||
command: nextflow run tests/software/gatk4/mergevcfs -entry test_gatk4_mergevcfs_refdict -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4_mergevcfs
|
||||
- gatk4/mergevcfs
|
||||
- gatk4
|
||||
- gatk4_mergevcfs_refdict
|
||||
- gatk4/mergevcfs_refdict
|
||||
files:
|
||||
- path: output/gatk4/test.merged.vcf.gz
|
||||
md5sum: ff48f175e26db2d4b2957762f6d1c715
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/gatk4/revertsam -entry test_gatk4_revertsam -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4_revertsam
|
||||
- gatk4/revertsam
|
||||
files:
|
||||
- path: output/gatk4/test.reverted.bam
|
||||
md5sum: f778310b18b83b49929eb648594f96dc
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4_samtofastq
|
||||
- gatk4/samtofastq
|
||||
- gatk4_samtofastq_single_end
|
||||
files:
|
||||
- path: output/gatk4/test.fastq.gz
|
||||
|
|
@ -12,7 +12,7 @@
|
|||
command: nextflow run tests/software/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4_samtofastq
|
||||
- gatk4/samtofastq
|
||||
- gatk4_samtofastq_paired_end
|
||||
files:
|
||||
- path: output/gatk4/test_1.fastq.gz
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4
|
||||
- gatk4_splitncigarreads
|
||||
- gatk4/splitncigarreads
|
||||
files:
|
||||
- path: output/gatk4/test.split_cigar.bam
|
||||
md5sum: a8473bd4abc7b13751fc51b92531da4c
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: gatk4 variantfiltration test_gatk4_variantfiltration
|
||||
command: nextflow run tests/software/gatk4/variantfiltration -entry test_gatk4_variantfiltration -c tests/config/nextflow.config
|
||||
tags:
|
||||
- gatk4_variantfiltration
|
||||
- gatk4/variantfiltration
|
||||
- gatk4
|
||||
files:
|
||||
- path: output/gatk4/test.filtered.vcf
|
||||
|
|
|
|||
|
|
@ -2,6 +2,6 @@
|
|||
command: nextflow run tests/software/homer/annotatepeaks -entry test_homer_annotatepeaks -c tests/config/nextflow.config
|
||||
tags:
|
||||
- homer
|
||||
- homer_annotatepeaks
|
||||
- homer/annotatepeaks
|
||||
files:
|
||||
- path: output/homer/test.annotatePeaks.txt
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/ivar/consensus -entry test_ivar_consensus -c tests/config/nextflow.config
|
||||
tags:
|
||||
- ivar
|
||||
- ivar_consensus
|
||||
- ivar/consensus
|
||||
files:
|
||||
- path: output/ivar/test.fa
|
||||
md5sum: 9e21a64818f4302b4dece5480fa5e8b8
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/ivar/trim -entry test_ivar_trim -c tests/config/nextflow.config
|
||||
tags:
|
||||
- ivar
|
||||
- ivar_trim
|
||||
- ivar/trim
|
||||
files:
|
||||
- path: output/ivar/test.bam
|
||||
md5sum: 8705d032b28a1c3dbfe78fa762a2132f
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c tests/config/nextflow.config
|
||||
tags:
|
||||
- ivar
|
||||
- ivar_variants
|
||||
- ivar/variants
|
||||
files:
|
||||
- path: output/ivar/test.tsv
|
||||
md5sum: 728f1430f2402861396d9953465ac706
|
||||
|
|
@ -11,7 +11,7 @@
|
|||
command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c tests/config/nextflow.config --save_mpileup
|
||||
tags:
|
||||
- ivar
|
||||
- ivar_variants
|
||||
- ivar/variants
|
||||
files:
|
||||
- path: output/ivar/test.tsv
|
||||
md5sum: 728f1430f2402861396d9953465ac706
|
||||
|
|
@ -22,7 +22,7 @@
|
|||
command: nextflow run ./tests/software/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup
|
||||
tags:
|
||||
- ivar
|
||||
- ivar_variants
|
||||
- ivar/variants
|
||||
files:
|
||||
- path: output/ivar/test.tsv
|
||||
md5sum: 7b59146132a60da58444bebffc3c2577
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/kallisto/index -entry test_kallisto_index -c tests/config/nextflow.config
|
||||
tags:
|
||||
- kallisto
|
||||
- kallisto_index
|
||||
- kallisto/index
|
||||
files:
|
||||
- path: output/kallisto/kallisto
|
||||
md5sum: bf8a58d329dddc96f0c32f7823bc0310
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/kraken2/run -entry test_kraken2_run_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- kraken2
|
||||
- kraken2_run
|
||||
- kraken2/run
|
||||
- kraken2_run_single_end
|
||||
files:
|
||||
- path: output/kraken2/test.classified.fastq.gz
|
||||
|
|
@ -16,7 +16,7 @@
|
|||
command: nextflow run ./tests/software/kraken2/run -entry test_kraken2_run_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- kraken2
|
||||
- kraken2_run
|
||||
- kraken2/run
|
||||
- kraken2_run_paired_end
|
||||
files:
|
||||
- path: output/kraken2/test.classified_1.fastq.gz
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/methyldackel/extract -entry test_methyldackel_extract -c tests/config/nextflow.config
|
||||
tags:
|
||||
- methyldackel
|
||||
- methyldackel_extract
|
||||
- methyldackel/extract
|
||||
files:
|
||||
- path: output/methyldackel/test_methylated_paired_end.sorted_CpG.bedGraph
|
||||
md5sum: d7c637e2ef20de401fc610206f6bf6b7
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/methyldackel/mbias -entry test_methyldackel_mbias -c tests/config/nextflow.config
|
||||
tags:
|
||||
- methyldackel
|
||||
- methyldackel_mbias
|
||||
- methyldackel/mbias
|
||||
files:
|
||||
- path: output/methyldackel/test.mbias.txt
|
||||
md5sum: 357bb944dc2cdffcc47fa0d34376e016
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- minimap2
|
||||
- minimap2_align
|
||||
- minimap2/align
|
||||
- minimap2_align_single_end
|
||||
files:
|
||||
- path: ./output/minimap2/test.paf
|
||||
|
|
@ -12,7 +12,7 @@
|
|||
command: nextflow run ./tests/software/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- minimap2
|
||||
- minimap2_align
|
||||
- minimap2/align
|
||||
- minimap2_align_paired_end
|
||||
files:
|
||||
- path: ./output/minimap2/test.paf
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: picard collectwgsmetrics test_picard_collectwgsmetrics
|
||||
command: nextflow run tests/software/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c tests/config/nextflow.config
|
||||
tags:
|
||||
- picard_collectwgsmetrics
|
||||
- picard/collectwgsmetrics
|
||||
- picard
|
||||
files:
|
||||
- path: output/picard/test.CollectWgsMetrics.coverage_metrics
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_sorted_bam -c tests/config/nextflow.config
|
||||
tags:
|
||||
- picard
|
||||
- picard_markduplicates
|
||||
- picard/markduplicates
|
||||
files:
|
||||
- path: ./output/picard/test.MarkDuplicates.metrics.txt
|
||||
- path: ./output/picard/test.bam
|
||||
|
|
@ -12,6 +12,6 @@
|
|||
command: nextflow run ./tests/software/picard/markduplicates -entry test_picard_markduplicates_unsorted_bam -c tests/config/nextflow.config
|
||||
tags:
|
||||
- picard
|
||||
- picard_markduplicates
|
||||
- picard/markduplicates
|
||||
- should fail
|
||||
exit_code: 1
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/picard/mergesamfiles -entry test_picard_mergesamfiles -c tests/config/nextflow.config
|
||||
tags:
|
||||
- picard
|
||||
- picard_mergesamfiles
|
||||
- picard/mergesamfiles
|
||||
files:
|
||||
- path: ./output/picard/test.bam
|
||||
md5sum: b8bd6c22f36c6ebc91bca98bd637a2eb
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- preseq
|
||||
- preseq_lcextrap
|
||||
- preseq/lcextrap
|
||||
- preseq_lcextrap_single_end
|
||||
files:
|
||||
- path: output/preseq/test.ccurve.txt
|
||||
|
|
@ -13,7 +13,7 @@
|
|||
command: nextflow run ./tests/software/preseq/lcextrap -entry test_preseq_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- preseq
|
||||
- preseq_lcextrap
|
||||
- preseq/lcextrap
|
||||
- preseq_lcextrap_paired_end
|
||||
files:
|
||||
- path: output/preseq/test.ccurve.txt
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/qualimap/bamqc -entry test_qualimap_bamqc -c tests/config/nextflow.config
|
||||
tags:
|
||||
- qualimap
|
||||
- qualimap_bamqc
|
||||
- qualimap/bamqc
|
||||
files:
|
||||
- path: ./output/qualimap/test/qualimapReport.html
|
||||
- path: ./output/qualimap/test/genome_results.txt
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/salmon/index -entry test_salmon_index -c tests/config/nextflow.config
|
||||
tags:
|
||||
- salmon
|
||||
- salmon_index
|
||||
- salmon/index
|
||||
files:
|
||||
- path: ./output/index/salmon/ref_indexing.log
|
||||
- path: ./output/index/salmon/refseq.bin
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- salmon
|
||||
- salmon_quant
|
||||
- salmon/quant
|
||||
- salmon_quant_single_end
|
||||
files:
|
||||
- path: ./output/salmon/test/cmd_info.json
|
||||
|
|
@ -54,7 +54,7 @@
|
|||
command: nextflow run ./tests/software/salmon/quant -entry test_salmon_quant_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- salmon
|
||||
- salmon_quant
|
||||
- salmon/quant
|
||||
- salmon_quant_paired_end
|
||||
files:
|
||||
- path: ./output/salmon/test/cmd_info.json
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/samtools/faidx -entry test_samtools_faidx -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools_faidx
|
||||
- samtools/faidx
|
||||
files:
|
||||
- path: output/samtools/genome.fasta.fai
|
||||
md5sum: 9da2a56e2853dc8c0b86a9e7229c9fe5
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/samtools/fastq -entry test_samtools_fastq -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools_fastq
|
||||
- samtools/fastq
|
||||
files:
|
||||
- path: output/samtools/test_2.fastq.gz
|
||||
md5sum: 229daf1a62d114cae42c65801e8c0114
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/samtools/flagstat -entry test_samtools_flagstat -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools_flagstat
|
||||
- samtools/flagstat
|
||||
files:
|
||||
- path: ./output/samtools/test_paired_end.sorted.bam.flagstat
|
||||
md5sum: 6d7934c303b15ce473f64d502b79984e
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/samtools/idxstats -entry test_samtools_idxstats -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools_idxstats
|
||||
- samtools/idxstats
|
||||
files:
|
||||
- path: ./output/samtools/test_paired_end.sorted.bam.idxstats
|
||||
md5sum: df60a8c8d6621100d05178c93fb053a2
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/samtools/index -entry test_samtools_index -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools_index
|
||||
- samtools/index
|
||||
files:
|
||||
- path: output/samtools/test_paired_end.sorted.bam.bai
|
||||
md5sum: 704c10dd1326482448ca3073fdebc2f4
|
||||
|
|
|
|||
|
|
@ -2,6 +2,6 @@
|
|||
command: nextflow run ./tests/software/samtools/merge -entry test_samtools_merge -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools_merge
|
||||
- samtools/merge
|
||||
files:
|
||||
- path: output/samtools/test_merged.bam
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools_mpileup
|
||||
- samtools/mpileup
|
||||
files:
|
||||
- path: ./output/samtools/test.mpileup
|
||||
md5sum: 56c4cd5a4ecb7d6364878818f46ae256
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/samtools/sort -entry test_samtools_sort -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools_sort
|
||||
- samtools/sort
|
||||
files:
|
||||
- path: output/samtools/test.bam
|
||||
md5sum: 7e32f47768f922a73ccec4dc24db1973
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/samtools/stats -entry test_samtools_stats -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools_stats
|
||||
- samtools/stats
|
||||
files:
|
||||
- path: ./output/samtools/test_paired_end.sorted.bam.stats
|
||||
md5sum: 5f12c46ae4491b48611194c94093ebfb
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/samtools/view -entry test_samtools_view -c tests/config/nextflow.config
|
||||
tags:
|
||||
- samtools
|
||||
- samtools_view
|
||||
- samtools/view
|
||||
files:
|
||||
- path: output/samtools/test.bam
|
||||
md5sum: 8fb1e82f76416e9e30fc6b2357e2cf13
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/seacr/callpeak -entry test_seacr_callpeak -c tests/config/nextflow.config
|
||||
tags:
|
||||
- seacr
|
||||
- seacr_callpeak
|
||||
- seacr/callpeak
|
||||
files:
|
||||
- path: output/seacr/test_1.stringent.bed
|
||||
md5sum: 3ac70475669eb6a7b8ca89e19a08a28e
|
||||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_length -c tests/config/nextflow.config
|
||||
tags:
|
||||
- seqkit
|
||||
- seqkit_split2
|
||||
- seqkit/split2
|
||||
- seqkit_split2_single_end
|
||||
- length
|
||||
files:
|
||||
|
|
@ -16,7 +16,7 @@
|
|||
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
|
||||
tags:
|
||||
- seqkit
|
||||
- seqkit_split2
|
||||
- seqkit/split2
|
||||
- seqkit_split2_single_end
|
||||
- size
|
||||
files:
|
||||
|
|
@ -29,7 +29,7 @@
|
|||
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
|
||||
tags:
|
||||
- seqkit
|
||||
- seqkit_split2
|
||||
- seqkit/split2
|
||||
- seqkit_split2_single_end
|
||||
- part
|
||||
files:
|
||||
|
|
@ -44,7 +44,7 @@
|
|||
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
|
||||
tags:
|
||||
- seqkit
|
||||
- seqkit_split2
|
||||
- seqkit/split2
|
||||
- seqkit_split2_paired_end
|
||||
- length
|
||||
files:
|
||||
|
|
@ -61,7 +61,7 @@
|
|||
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
|
||||
tags:
|
||||
- seqkit
|
||||
- seqkit_split2
|
||||
- seqkit/split2
|
||||
- seqkit_split2_paired_end
|
||||
- size
|
||||
files:
|
||||
|
|
@ -78,7 +78,7 @@
|
|||
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
|
||||
tags:
|
||||
- seqkit
|
||||
- seqkit_split2
|
||||
- seqkit/split2
|
||||
- seqkit_split2_paired_end
|
||||
- part
|
||||
files:
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/seqwish/induce -entry test_seqwish_induce -c tests/config/nextflow.config
|
||||
tags:
|
||||
- seqwish
|
||||
- seqwish_induce
|
||||
- seqwish/induce
|
||||
files:
|
||||
- path: output/seqwish/test.gfa
|
||||
md5sum: 216a02d3aca322a457c31a62c628548e
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/shovill -entry test_shovill -c tests/config/nextflow.config
|
||||
tags:
|
||||
- shovill
|
||||
- shovill_spades
|
||||
- shovill/spades
|
||||
files:
|
||||
- path: output/shovill/contigs.gfa
|
||||
md5sum: 277af5d8ae8a0d2432db59a316226828
|
||||
|
|
@ -17,7 +17,7 @@
|
|||
command: nextflow run ./tests/software/shovill -entry test_shovill_megahit -c tests/config/nextflow.config
|
||||
tags:
|
||||
- shovill
|
||||
- shovill_megahit
|
||||
- shovill/megahit
|
||||
files:
|
||||
- path: output/shovill/shovill.corrections
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
|
|
@ -31,7 +31,7 @@
|
|||
command: nextflow run ./tests/software/shovill -entry test_shovill_skesa -c tests/config/nextflow.config
|
||||
tags:
|
||||
- shovill
|
||||
- shovill_skesa
|
||||
- shovill/skesa
|
||||
files:
|
||||
- path: output/shovill/shovill.corrections
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
|
|
@ -45,7 +45,7 @@
|
|||
command: nextflow run ./tests/software/shovill -entry test_shovill_velvet -c tests/config/nextflow.config
|
||||
tags:
|
||||
- shovill
|
||||
- shovill_velvet
|
||||
- shovill/velvet
|
||||
files:
|
||||
# MD5sum not reproducible (timestamp, contig order)
|
||||
- path: output/shovill/contigs.fa
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/star/align -entry test_star_alignment_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- star
|
||||
- star_align
|
||||
- star/align
|
||||
- star_align_single_end
|
||||
files:
|
||||
- path: output/star/star/Genome
|
||||
|
|
@ -40,7 +40,7 @@
|
|||
command: nextflow run ./tests/software/star/align -entry test_star_alignment_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- star
|
||||
- star_align
|
||||
- star/align
|
||||
- star_align_paired_end
|
||||
files:
|
||||
- path: output/star/star/Genome
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/star/genomegenerate -entry test_star_genomegenerate -c tests/config/nextflow.config
|
||||
tags:
|
||||
- star
|
||||
- star_genomegenerate
|
||||
- star/genomegenerate
|
||||
files:
|
||||
- path: ./output/index/star/Genome
|
||||
md5sum: 323c992bac354f93073ce0fc43f222f8
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@
|
|||
command: nextflow run ./tests/software/strelka/germline -entry test_strelka_germline -c tests/config/nextflow.config
|
||||
tags:
|
||||
- strelka
|
||||
- strelka_germline
|
||||
- strelka/germline
|
||||
files:
|
||||
- path: output/strelka/strelka_test_variants.vcf.gz
|
||||
- path: output/strelka/strelka_test_variants.vcf.gz.tbi
|
||||
|
|
@ -14,7 +14,7 @@
|
|||
command: nextflow run ./tests/software/strelka/germline -entry test_strelka_germline_target_bed -c tests/config/nextflow.config
|
||||
tags:
|
||||
- strelka
|
||||
- strelka_germline
|
||||
- strelka/germline
|
||||
files:
|
||||
- path: output/strelka/strelka_test_variants.vcf.gz
|
||||
- path: output/strelka/strelka_test_variants.vcf.gz.tbi
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/tabix/bgzip -entry test_tabix_bgzip -c tests/config/nextflow.config
|
||||
tags:
|
||||
- tabix
|
||||
- tabix_bgzip
|
||||
- tabix/bgzip
|
||||
files:
|
||||
- path: ./output/tabix/test.vcf.gz
|
||||
md5sum: 0f1c94af3aa3e7e203d9e034ef6f8f4d
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_bed -c tests/config/nextflow.config
|
||||
tags:
|
||||
- tabix
|
||||
- tabix_tabix
|
||||
- tabix/tabix
|
||||
- bed
|
||||
files:
|
||||
- path: ./output/tabix/test.bed.gz.tbi
|
||||
|
|
@ -11,7 +11,7 @@
|
|||
command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_gff -c tests/config/nextflow.config
|
||||
tags:
|
||||
- tabix
|
||||
- tabix_tabix
|
||||
- tabix/tabix
|
||||
- gff
|
||||
files:
|
||||
- path: ./output/tabix/genome.gff3.gz.tbi
|
||||
|
|
@ -20,7 +20,7 @@
|
|||
command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
|
||||
tags:
|
||||
- tabix
|
||||
- tabix_tabix
|
||||
- tabix/tabix
|
||||
- vcf
|
||||
files:
|
||||
- path: output/tabix/test.vcf.gz.tbi
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run ./tests/software/tiddit/sv -entry test_tiddit_sv -c tests/config/nextflow.config
|
||||
tags:
|
||||
- tiddit
|
||||
- tiddit_sv
|
||||
- tiddit/sv
|
||||
- vcf
|
||||
files:
|
||||
- path: output/tiddit/test.ploidy.tab
|
||||
|
|
@ -16,7 +16,7 @@
|
|||
command: nextflow run ./tests/software/tiddit/sv -entry test_tiddit_sv_no_ref -c tests/config/nextflow.config
|
||||
tags:
|
||||
- tiddit
|
||||
- tiddit_sv
|
||||
- tiddit/sv
|
||||
- vcf
|
||||
files:
|
||||
- path: output/tiddit/test.ploidy.tab
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: ucsc bed12tobigbed
|
||||
command: nextflow run ./tests/software/ucsc/bed12tobigbed -entry test_ucsc_bed12tobigbed -c tests/config/nextflow.config
|
||||
tags:
|
||||
- ucsc_bed12tobigbed
|
||||
- ucsc/bed12tobigbed
|
||||
files:
|
||||
- path: output/ucsc/test.bigBed
|
||||
md5sum: 98cf0d0baa3ae5a330c80afbb8bc2b18
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: ucsc bedgraphtobigwig
|
||||
command: nextflow run ./tests/software/ucsc/bedgraphtobigwig -entry test_ucsc_bedgraphtobigwig -c tests/config/nextflow.config
|
||||
tags:
|
||||
- ucsc_bedgraphtobigwig
|
||||
- ucsc/bedgraphtobigwig
|
||||
files:
|
||||
- path: output/ucsc/test.bigWig
|
||||
md5sum: 5346de25b01ecbff91b63178b3bfbeec
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
- name: yara index test_yara_index
|
||||
command: nextflow run tests/software/yara/index -entry test_yara_index -c tests/config/nextflow.config
|
||||
tags:
|
||||
- yara_index
|
||||
- yara/index
|
||||
- yara
|
||||
files:
|
||||
- path: output/index/yara/yara.rid.limits
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
command: nextflow run tests/software/yara/mapper -entry test_yara_single_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- yara_single_end
|
||||
- yara_mapper
|
||||
- yara/mapper
|
||||
- yara
|
||||
files:
|
||||
- path: output/yara/test.mapped.bam
|
||||
|
|
@ -36,7 +36,7 @@
|
|||
- name: yara mapper test_yara_paired_end
|
||||
command: nextflow run tests/software/yara/mapper -entry test_yara_paired_end -c tests/config/nextflow.config
|
||||
tags:
|
||||
- yara_mapper
|
||||
- yara/mapper
|
||||
- yara_paired_end
|
||||
- yara
|
||||
files:
|
||||
|
|
|
|||
Loading…
Reference in a new issue