mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-31 03:32:10 -05:00
Adding tests for bcftools
This commit is contained in:
JoseEspinosa
parent
579de3e038
commit
a3ce63c79c
8 changed files with 382 additions and 0 deletions
40
.github/workflows/bcftools_bgzip.yml
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40
.github/workflows/bcftools_bgzip.yml
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name: bcftools_bgzip
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on:
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push:
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paths:
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- software/bcftools/bgzip/**
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- .github/workflows/bcftools_bgzip.yml
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- tests/software/bcftools/**
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pull_request:
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paths:
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- software/bcftools/bgzip/**
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- .github/workflows/bcftools_bgzip.yml
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- tests/software/bcftools/**
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jobs:
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ci_test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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nxf_version: [20.11.0-edge]
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
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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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# Test the module
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- run: pytest --tag bcftools_bgzip --symlink --wt 2
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44
.github/workflows/bcftools_consensus.yml
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44
.github/workflows/bcftools_consensus.yml
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name: bcftools_consensus
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on:
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push:
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paths:
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- software/bcftools/bgzip/**
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- software/bcftools/tabix/**
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- software/bcftools/consensus/**
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- .github/workflows/bcftools_consensus.yml
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- tests/software/bcftools/**
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pull_request:
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paths:
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- software/bcftools/bgzip/**
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- software/bcftools/tabix/**
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- software/bcftools/consensus/**
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- .github/workflows/bcftools_consensus.yml
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- tests/software/bcftools/**
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jobs:
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ci_test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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nxf_version: [20.11.0-edge]
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
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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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# Test the module
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- run: pytest --tag bcftools_consensus --symlink --wt 2
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40
.github/workflows/bcftools_filter.yml
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40
.github/workflows/bcftools_filter.yml
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name: bcftools_filter
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on:
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push:
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paths:
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- software/bcftools/filter/**
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- .github/workflows/bcftools_filter.yml
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- tests/software/bcftools/**
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pull_request:
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paths:
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- software/bcftools/filter/**
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- .github/workflows/bcftools_filter.yml
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- tests/software/bcftools/**
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jobs:
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ci_test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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nxf_version: [20.11.0-edge]
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
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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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# Test the module
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- run: pytest --tag bcftools_filter --symlink --wt 2
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40
.github/workflows/bcftools_stats.yml
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40
.github/workflows/bcftools_stats.yml
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name: bcftools_stats
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on:
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push:
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paths:
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- software/bcftools/stats/**
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- .github/workflows/bcftools_stats.yml
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- tests/software/bcftools/**
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pull_request:
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paths:
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- software/bcftools/stats/**
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- .github/workflows/bcftools_stats.yml
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- tests/software/bcftools/**
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jobs:
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ci_test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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nxf_version: [20.11.0-edge]
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
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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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# Test the module
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- run: pytest --tag bcftools_stats --symlink --wt 2
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42
.github/workflows/bcftools_tabix.yml
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42
.github/workflows/bcftools_tabix.yml
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name: bcftools_tabix
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on:
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push:
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paths:
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- software/bcftools/bgzip/**
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- software/bcftools/tabix/**
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- .github/workflows/bcftools_tabix.yml
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- tests/software/bcftools/**
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pull_request:
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paths:
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- software/bcftools/bgzip/**
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- software/bcftools/tabix/**
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- .github/workflows/bcftools_tabix.yml
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- tests/software/bcftools/**
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jobs:
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ci_test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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nxf_version: [20.11.0-edge]
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
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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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# Test the module
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- run: pytest --tag bcftools_tabix --symlink --wt 2
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64
output/bcftools/test.bcftools_stats.txt
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64
output/bcftools/test.bcftools_stats.txt
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# This file was produced by bcftools stats (1.11+htslib-1.11) and can be plotted using plot-vcfstats.
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# The command line was: bcftools stats test.vcf
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#
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# Definition of sets:
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# ID [2]id [3]tab-separated file names
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ID 0 test.vcf
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# SN, Summary numbers:
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# number of records .. number of data rows in the VCF
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# number of no-ALTs .. reference-only sites, ALT is either "." or identical to REF
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# number of SNPs .. number of rows with a SNP
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# number of MNPs .. number of rows with a MNP, such as CC>TT
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# number of indels .. number of rows with an indel
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# number of others .. number of rows with other type, for example a symbolic allele or
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# a complex substitution, such as ACT>TCGA
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# number of multiallelic sites .. number of rows with multiple alternate alleles
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# number of multiallelic SNP sites .. number of rows with multiple alternate alleles, all SNPs
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#
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# Note that rows containing multiple types will be counted multiple times, in each
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# counter. For example, a row with a SNP and an indel increments both the SNP and
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# the indel counter.
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#
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# SN [2]id [3]key [4]value
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SN 0 number of samples: 1
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SN 0 number of records: 15
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SN 0 number of no-ALTs: 2
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SN 0 number of SNPs: 7
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SN 0 number of MNPs: 0
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SN 0 number of indels: 3
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SN 0 number of others: 3
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SN 0 number of multiallelic sites: 1
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SN 0 number of multiallelic SNP sites: 1
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# TSTV, transitions/transversions:
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# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
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TSTV 0 3 5 0.60 3 4 0.75
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# SiS, Singleton stats:
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# SiS [2]id [3]allele count [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
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SiS 0 1 8 3 5 3 0 0 3
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# AF, Stats by non-reference allele frequency:
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# AF [2]id [3]allele frequency [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable
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AF 0 0.000000 8 3 5 3 0 0 3
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# QUAL, Stats by quality:
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# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels
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QUAL 0 998 7 3 4 3
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# IDD, InDel distribution:
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# IDD [2]id [3]length (deletions negative) [4]number of sites [5]number of genotypes [6]mean VAF
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IDD 0 -2 1 0 .
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IDD 0 3 1 0 .
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IDD 0 8 1 0 .
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# ST, Substitution types:
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# ST [2]id [3]type [4]count
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ST 0 A>C 1
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ST 0 A>G 0
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ST 0 A>T 0
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ST 0 C>A 2
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ST 0 C>G 0
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ST 0 C>T 1
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ST 0 G>A 1
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ST 0 G>C 0
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ST 0 G>T 0
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ST 0 T>A 2
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ST 0 T>C 1
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ST 0 T>G 0
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# DP, Depth distribution
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# DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%)
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64
tests/software/bcftools/main.nf
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64
tests/software/bcftools/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BCFTOOLS_FILTER } from '../../../software/bcftools/filter/main.nf' addParams( options: [:] )
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include { BCFTOOLS_STATS } from '../../../software/bcftools/stats/main.nf' addParams( options: [:] )
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include { BCFTOOLS_BGZIP } from '../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
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include { BCFTOOLS_TABIX } from '../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
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include { BCFTOOLS_CONSENSUS } from '../../../software/bcftools/consensus/main.nf' addParams( options: [:] )
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workflow test_bcftools_filter {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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BCFTOOLS_FILTER ( input )
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}
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workflow test_bcftools_stats {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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BCFTOOLS_STATS ( input )
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}
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workflow test_bcftools_bgzip {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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BCFTOOLS_BGZIP ( input )
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}
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workflow test_bcftools_tabix {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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BCFTOOLS_BGZIP ( input )
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BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
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}
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workflow test_bcftools_consensus {
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def input = []
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input = [ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]
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def fasta = []
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fasta = Channel.of ([ [ id:'test' ], // meta map
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file("${launchDir}/tests/data/vcf/test.consensus.fa", checkIfExists: true) ])
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BCFTOOLS_BGZIP ( input )
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BCFTOOLS_TABIX ( BCFTOOLS_BGZIP.out.vcf )
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BCFTOOLS_CONSENSUS ( BCFTOOLS_BGZIP.out.vcf
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.join( BCFTOOLS_TABIX.out.tbi, by: [0] )
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.join( fasta, by: [0] ) )
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}
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48
tests/software/bcftools/test.yml
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48
tests/software/bcftools/test.yml
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- name: Run bcftools filter test workflow
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command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_filter -c tests/config/nextflow.config
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tags:
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- bcftools
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- bcftools_filter
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files:
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- path: output/bcftools/test.vcf.gz
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md5sum: b994e60162fd97c118ddd45b08018d98
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- name: Run bcftools stats test workflow
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command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_stats -c tests/config/nextflow.config
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tags:
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- bcftools
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- bcftools_stats
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files:
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- path: output/bcftools/test.bcftools_stats.txt
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md5sum: abfc6a90f84e24b2cc7e92cbce06200a
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- name: Run bcftools bgzip test workflow
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command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_bgzip -c tests/config/nextflow.config
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tags:
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- bcftools
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- bcftools_bgzip
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files:
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- path: output/bcftools/test.vcf.gz
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md5sum: eb75ae1f08a1884f8edc59ed423471a2
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- name: Run bcftools tabix test workflow
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command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_tabix -c tests/config/nextflow.config
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tags:
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- bcftools
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- bcftools_tabix
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files:
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- path: output/bcftools/test.vcf.gz.tbi
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md5sum: 06d52177f819730dd409157914534e8d
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- name: Run bcftools consensus test workflow
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command: nextflow run ./tests/software/bcftools/ -profile docker -entry test_bcftools_consensus -c tests/config/nextflow.config
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tags:
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- bcftools
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- bcftools_consensus
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files:
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- path: output/bcftools/test.vcf.gz
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md5sum: eb75ae1f08a1884f8edc59ed423471a2
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- path: output/bcftools/test.vcf.gz.tbi
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md5sum: 06d52177f819730dd409157914534e8d
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- path: output/bcftools/test.fa
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md5sum: c9e7ac4537756a0b33bcf17117f9a065
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