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ci(samtools): Run tests with pytest-workflow

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Edmund Miller 2020-11-24 20:24:34 -06:00
parent b2cd464ad3
commit 445498d0c3
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4 changed files with 56 additions and 32 deletions
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22
.github/workflows/software/samtools_idxstats.yml vendored
View file

@ -17,14 +17,20 @@ jobs:
env: env:
NXF_ANSI_LOG: false NXF_ANSI_LOG: false
steps: steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2 - name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow - name: Set up Python
run: | uses: actions/setup-python@v2
export NXF_VER="20.07.1" with:
wget -qO- get.nextflow.io | bash python-version: "3.x"
sudo mv nextflow /usr/local/bin/ - name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module # Test the module
- run: nextflow run ./software/samtools/idxstats/test/ -profile docker - run: pytest --tag samtools_idxstats --symlink --wt 2

22
.github/workflows/software/samtools_index.yml vendored
View file

@ -17,14 +17,20 @@ jobs:
env: env:
NXF_ANSI_LOG: false NXF_ANSI_LOG: false
steps: steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2 - name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow - name: Set up Python
run: | uses: actions/setup-python@v2
export NXF_VER="20.07.1" with:
wget -qO- get.nextflow.io | bash python-version: "3.x"
sudo mv nextflow /usr/local/bin/ - name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module # Test the module
- run: nextflow run ./software/samtools/index/test/ -profile docker - run: pytest --tag samtools_index --symlink --wt 2

22
.github/workflows/software/samtools_sort.yml vendored
View file

@ -17,14 +17,20 @@ jobs:
env: env:
NXF_ANSI_LOG: false NXF_ANSI_LOG: false
steps: steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2 - name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow - name: Set up Python
run: | uses: actions/setup-python@v2
export NXF_VER="20.07.1" with:
wget -qO- get.nextflow.io | bash python-version: "3.x"
sudo mv nextflow /usr/local/bin/ - name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module # Test the module
- run: nextflow run ./software/samtools/sort/test/ -profile docker - run: pytest --tag samtools_sort --symlink --wt 2

22
.github/workflows/software/samtools_stats.yml vendored
View file

@ -17,14 +17,20 @@ jobs:
env: env:
NXF_ANSI_LOG: false NXF_ANSI_LOG: false
steps: steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v2 - name: Install Nextflow
run: |
export NXF_VER="20.07.1"
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Install Nextflow - name: Set up Python
run: | uses: actions/setup-python@v2
export NXF_VER="20.07.1" with:
wget -qO- get.nextflow.io | bash python-version: "3.x"
sudo mv nextflow /usr/local/bin/ - name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow
# Test the module # Test the module
- run: nextflow run ./software/samtools/stats/test/ -profile docker - run: pytest --tag samtools_stats --symlink --wt 2