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Adding tbp-parser to TheiaProk #476

Adding tbp-parser to TheiaProk

Adding tbp-parser to TheiaProk #476

#
# This workflow will run on Pushes and Pull Requests against the main branch. It
# will run pytest with MiniWDL and Cromwell for any workflows with a change to
# them or associated tasks.
#
name: Pytest Workflows
on:
push:
branches: [main]
pull_request:
branches: [main]
jobs:
changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
# Expose workflows with changes
workflows: ${{ steps.filter.outputs.changes }}
steps:
# Checkout the repo
- uses: actions/checkout@v3
# Select workflows with changes
- uses: dorny/paths-filter@v2
id: filter
with:
filters: "tests/config/pytest_filter.yml"
check:
runs-on: ubuntu-20.04
name: ${{ matrix.tag }} ${{ matrix.engine }}
needs: changes
if: ${{ needs.changes.outputs.workflows != '[]' && needs.changes.outputs.workflows != '' }}
strategy:
fail-fast: false
matrix:
# For every workflow, test it with MiniWDL and Cromwell
tag: ["${{ fromJson(needs.changes.outputs.workflows) }}"]
engine: ["miniwdl", "cromwell"]
defaults:
run:
# Play nicely with miniconda
shell: bash -l {0}
steps:
# Checkout the repo
- name: Checkout theiagen/public_health_bacterial_genomics
uses: actions/checkout@v3
# Import test data
- name: Pull Test Data from bactopia/bactopia-tests
uses: actions/checkout@v3
with:
repository: bactopia/bactopia-tests
path: bactopia-tests
# Setup Miniconda3
- name: Setup miniconda
uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: actions
auto-activate-base: false
# Depends and env info (mostly for debug)
# rm -rf commands as recommended here: https://github.com/actions/runner-images/issues/2840#issuecomment-1284059930
- name: Install Dependencies and create storage space
run: |
conda install -y -c conda-forge -c bioconda cromwell miniwdl=1.5.2 'python>=3.7' pytest pytest-workflow 'importlib-metadata<=4.13.0'
conda clean -a -y
uname -a && env
sudo rm -rf /usr/share/dotnet
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: Test ${{ matrix.tag }}
run: TMPDIR=~ pytest --tag ${{ matrix.tag }}_${{ matrix.engine }} --symlink --kwdof --color=yes
- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v3
with:
name: logs-${{ matrix.engine }}
path: |
/home/runner/pytest_workflow_*/**/stdout*
/home/runner/pytest_workflow_*/**/stderr*
/home/runner/pytest_workflow_*/**/script*
/home/runner/pytest_workflow_*/**/rc
/home/runner/pytest_workflow_*/**/command
/home/runner/pytest_workflow_*/**/*.txt
/home/runner/pytest_workflow_*/**/*.log
/home/runner/pytest_workflow_*/**/*.out
/home/runner/pytest_workflow_*/**/*.err
/home/runner/pytest_workflow_*/**/DATE
/home/runner/pytest_workflow_*/**/VERSION
!/home/runner/pytest_workflow_*/**/*.bam*
!/home/runner/pytest_workflow_*/**/*.fastq.gz