nf-core_modules/.github/workflows/pytest-workflow.yml

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name: Pytest-workflow
on: [push, pull_request]
jobs:
changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
# Expose matched filters as job 'modules' output variable
modules: ${{ steps.filter.outputs.changes }}
steps:
- uses: actions/checkout@v2
- uses: dorny/paths-filter@v2
id: filter
with:
filters: "tests/config/pytest_modules.yml"
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test:
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runs-on: ubuntu-20.04
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name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
needs: changes
if: needs.changes.outputs.modules != '[]'
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strategy:
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fail-fast: false
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matrix:
nxf_version: ["21.04.0"]
tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
profile: ["docker", "singularity", "conda"]
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env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
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- uses: actions/cache@v2
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow
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- uses: actions/cache@v2
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
restore-keys: |
${{ runner.os }}-nextflow-
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
- name: Set up Singularity
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-singularity@v5
with:
singularity-version: 3.7.1
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- name: Setup miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
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channels: conda-forge,bioconda,defaults
python-version: ${{ matrix.python-version }}
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- name: Conda clean
if: matrix.profile == 'conda'
run: conda clean -a
# Test the module
- name: Run pytest-workflow
# only use one thread for pytest-workflow to avoid race condition on conda cache.
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof
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- name: Upload logs on failure
if: failure()
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uses: actions/upload-artifact@v2
with:
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name: logs-${{ matrix.tags }}-${{ matrix.profile }}-${{ matrix.nxf_version }}
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path: |
/home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err
/home/runner/pytest_workflow_*/*/work