From 1030a7277f6ee15507e65f8063534092ee979378 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Wed, 10 Mar 2021 16:05:54 +0100
Subject: [PATCH] Only include a single test
---
.github/workflows/ci.yml | 39 ++++++++++-----------------------------
1 file changed, 10 insertions(+), 29 deletions(-)
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index a60978d..3b63ee6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,34 +14,7 @@ jobs:
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
@@ -61,7 +34,7 @@ jobs:
run: >-
pytest --keep-workflow-wd-on-fail --tag ${{ matrix.test }} --symlink tests/
- - name: Check job stderr messages in case of failure
+ - name: Check pipeline stderr messages in case of failure
if: ${{ failure() }}
run: >-
bash -c '
@@ -69,7 +42,7 @@ jobs:
echo $file; cat $file
done
'
- - name: Check job stdout messages in case of failure
+ - name: Check pipeline stdout messages in case of failure
if: ${{ failure() }}
run: >-
bash -c '
@@ -77,3 +50,11 @@ jobs:
echo $file; cat $file
done
'
+ - name: Check all job log files in case of failure
+ if: ${{ failure() }}
+ run: >-
+ bash -c '
+ for file in $(find /tmp/pytest_workflow_*/log/ -type f); do
+ echo $file; cat $file
+ done
+ '
--
GitLab