From 914481805d1b7c9d538d594bc5afff2345dc7f74 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 9 Jun 2022 14:07:23 +0200 Subject: [PATCH 1/2] improve CI --- .github/workflows/ci.yml | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cda22a177..0a6208330 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -54,6 +54,7 @@ jobs: - "split_fastq" - "targeted" - "tumor_normal_pair" + steps: - name: Check out pipeline code uses: actions/checkout@v2 @@ -68,15 +69,21 @@ jobs: wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ nextflow self-update + - name: Set up Python uses: actions/setup-python@v2 with: python-version: "3.x" + - name: Install dependencies run: python -m pip install --upgrade pip pytest-workflow - name: Run pipeline with tests settings - run: pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes + uses: Wandalen/wretry.action@v1.0.11 + with: + command: pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes + attempt_limit: 3 + - name: Output log on failure if: failure() run: | From 91516b5dac32df93ef675656761cb96031cb18ff Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 9 Jun 2022 14:11:14 +0200 Subject: [PATCH 2/2] update CHANGELOG [skip ci] --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index df995e232..da9fca265 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -72,7 +72,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#334](https://github.com/nf-core/sarek/pull/334) - Sync `dsl2` and `dev` branches - [#342](https://github.com/nf-core/sarek/pull/342) - Update `README.md` - [#386](https://github.com/nf-core/sarek/pull/386) - Annotation is back -- [#410](https://github.com/nf-core/sarek/pull/410), [#412](https://github.com/nf-core/sarek/pull/412) - Update `CI` tests +- [#410](https://github.com/nf-core/sarek/pull/410), [#412](https://github.com/nf-core/sarek/pull/412), [#584](https://github.com/nf-core/sarek/pull/584) - Update `CI` tests - [#418](https://github.com/nf-core/sarek/pull/418) - Fix `known_sites` channels - [#432](https://github.com/nf-core/sarek/pull/432), [#457](https://github.com/nf-core/sarek/pull/457) - Sort before `tabix index` - [#454](https://github.com/nf-core/sarek/pull/454) - Input is optional (can actually be found automatically by `Sarek` if previously run)