mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-31 11:42:12 -05:00
Fixed testing, rebased
This commit is contained in:
sruthipsuresh
parent
e360617ac6
commit
84b66e4f38
7 changed files with 24 additions and 240 deletions
24
.github/filters.yml
vendored
24
.github/filters.yml
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@ -144,3 +144,27 @@ trimgalore:
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ucsc_bedgraphtobigwig:
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- software/ucsc/bedgraphtobigwig/**
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- tests/software/ucsc/bedgraphtobigwig/**
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bedtools_complement:
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- software/bedtools/complement/**
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- tests/software/bedtools/**
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bedtools_genomecov:
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- software/bedtools/genomecov/**
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- tests/software/bedtools/**
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bedtools_intersect:
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- software/bedtools/intersect/**
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- tests/software/bedtools/**
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bedtools_merge:
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- software/bedtools/merge/**
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- tests/software/bedtools/**
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bedtools_slop:
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- software/bedtools/slop/**
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- tests/software/bedtools/**
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bedtools_sort:
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- software/bedtools/sort/**
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- tests/software/bedtools/**
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40
.github/workflows/bedtools_complement.yml
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40
.github/workflows/bedtools_complement.yml
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@ -1,40 +0,0 @@
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name: bedtools_complement
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on:
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push:
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paths:
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- software/bedtools/complement/**
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- .github/workflows/bedtools_complement.yml
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- tests/software/bedtools/**
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pull_request:
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paths:
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- software/bedtools/complement/**
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- .github/workflows/bedtools_complement.yml
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- tests/software/bedtools/**
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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 bedtools_complement --symlink --wt 2
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40
.github/workflows/bedtools_genomecov.yml
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40
.github/workflows/bedtools_genomecov.yml
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@ -1,40 +0,0 @@
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name: bedtools_genomecov
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on:
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push:
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paths:
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- software/bedtools/genomecov/**
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- .github/workflows/bedtools_genomecov.yml
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- tests/software/bedtools/**
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pull_request:
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paths:
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- software/bedtools/genomecov/**
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- .github/workflows/bedtools_genomecov.yml
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- tests/software/bedtools/**
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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 bedtools_genomecov --symlink --wt 2
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40
.github/workflows/bedtools_intersect.yml
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40
.github/workflows/bedtools_intersect.yml
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@ -1,40 +0,0 @@
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name: bedtools_intersect
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on:
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push:
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paths:
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- software/bedtools/intersect/**
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- .github/workflows/bedtools_intersect.yml
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- tests/software/bedtools/**
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pull_request:
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paths:
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- software/bedtools/intersect/**
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- .github/workflows/bedtools_intersect.yml
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- tests/software/bedtools/**
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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 bedtools_intersect --symlink --wt 2
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40
.github/workflows/bedtools_merge.yml
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40
.github/workflows/bedtools_merge.yml
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@ -1,40 +0,0 @@
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name: bedtools_merge
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on:
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push:
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paths:
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- software/bedtools/merge/**
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- .github/workflows/bedtools_merge.yml
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- tests/software/bedtools/**
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pull_request:
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paths:
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- software/bedtools/merge/**
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- .github/workflows/bedtools_merge.yml
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- tests/software/bedtools/**
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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 bedtools_merge --symlink --wt 2
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40
.github/workflows/bedtools_slop.yml
vendored
40
.github/workflows/bedtools_slop.yml
vendored
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@ -1,40 +0,0 @@
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name: bedtools_slop
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on:
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push:
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paths:
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- software/bedtools/slop/**
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- .github/workflows/bedtools_slop.yml
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- tests/software/bedtools/**
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pull_request:
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paths:
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- software/bedtools/slop/**
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- .github/workflows/bedtools_slop.yml
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- tests/software/bedtools/**
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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 bedtools_slop --symlink --wt 2
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40
.github/workflows/bedtools_sort.yml
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40
.github/workflows/bedtools_sort.yml
vendored
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@ -1,40 +0,0 @@
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name: bedtools_sort
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on:
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push:
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paths:
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- software/bedtools/sort/**
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- .github/workflows/bedtools_sort.yml
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- tests/software/bedtools/**
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pull_request:
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paths:
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- software/bedtools/sort/**
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- .github/workflows/bedtools_sort.yml
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- tests/software/bedtools/**
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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 bedtools_sort --symlink --wt 2
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