Commit b53a4948 authored by van den Berg's avatar van den Berg
Browse files

Add github workflows

parent 08281f79
Pipeline #5289 failed with stages
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### Checklist
- [ ] Pull request details were added to CHANGELOG.md.
- [ ] New tests have been added to the matrix section of the
.github/workflows/ci.yml file.
name: Continuous Integration
on: [push, pull_request]
defaults:
run:
# This is needed for miniconda, see:
# https://github.com/marketplace/actions/setup-miniconda#important.
shell: bash -l {0}
jobs:
tests:
runs-on: ubuntu-latest
strategy:
matrix:
test:
- sanity-snakemake
- sanity-snakemake-lint
- sanity-singularity
- sanity-no-reference
- sanity-reference-does-not-exist
- sanity-baits-only
- sanity-targets-only
- sanity-samples-overlapping-name
- sanity-multisample
- dry-run-vanilla
- dry-run-target-baits
- dry-run-bed-coverage
- dry-run-multisample
- integration-vanilla
- integration-small-scatter
- integration-refflat
- integration-all-on-target
- integration-gene-bedfile
- integration-two-known-sites
- integration-two-readgroups
- integration-two-samples
- integration-target-baits
- integration-bed-coverage
- integration-restrict_BQSR
- integration-targets-only
- integration-multisample
steps:
- uses: actions/checkout@v2
- uses: eWaterCycle/setup-singularity@v6
with:
singularity-version: 3.6.4
- uses: conda-incubator/setup-miniconda@v2.0.1
# https://github.com/conda-incubator/setup-miniconda.
with:
activate-environment: hutspot
environment-file: environment.yml
auto-activate-base: false
- name: Run test in conda evironment
# Use --symlink to limit disk usage.
run: >-
pytest --keep-workflow-wd-on-fail --tag ${{ matrix.test }} --symlink tests/
- name: Check job stderr messages in case of failure
if: ${{ failure() }}
run: >-
bash -c '
for file in $(find /tmp/pytest_workflow_* -name log.err); do
echo $file; cat $file
done
'
- name: Check job stdout messages in case of failure
if: ${{ failure() }}
run: >-
bash -c '
for file in $(find /tmp/pytest_workflow_* -name log.out); do
echo $file; cat $file
done
'
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