From b53a4948317a58d5f2a23e10fbc933320911af56 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Tue, 9 Mar 2021 17:12:57 +0100
Subject: [PATCH] Add github workflows
---
.github/PULL_REQUEST_TEMPLATE.md | 4 ++
.github/workflows/ci.yml | 79 ++++++++++++++++++++++++++++++++
2 files changed, 83 insertions(+)
create mode 100644 .github/PULL_REQUEST_TEMPLATE.md
create mode 100644 .github/workflows/ci.yml
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
new file mode 100644
index 0000000..93c5c5e
--- /dev/null
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -0,0 +1,4 @@
+### 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.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..05dc11e
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,79 @@
+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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