From 14a3120855c4f3cd6f9f7b555d4c4e53d7dc481b Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 2 Jun 2025 15:35:13 +0200 Subject: [PATCH 1/5] use yaml specific comment symbols --- .prettierignore | 1 + nf_core/pipeline-template/.github/workflows/nf-test.yml | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.prettierignore b/.prettierignore index f4a0781a1b..73e4c4e278 100644 --- a/.prettierignore +++ b/.prettierignore @@ -8,6 +8,7 @@ nf_core/pipeline-template/nextflow_schema.json nf_core/pipeline-template/modules.json nf_core/pipeline-template/tower.yml nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml +nf_core/pipeline-template/.github/workflows/nf-test.yml tests/data/pipeline_create_template_skip.yml # don't run on things handled by ruff *.py diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml index 3960965c8c..eeba2ad132 100644 --- a/nf_core/pipeline-template/.github/workflows/nf-test.yml +++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml @@ -34,7 +34,7 @@ env: jobs: nf-test-changes: name: nf-test-changes - runs-on: // {% endraw %}{% if is_nfcore %}use self-hosted runners + runs-on: #{% endraw %}{% if is_nfcore %} use self-hosted runners - runs-on=${{ github.run_id }}-nf-test-changes - runner=4cpu-linux-x64{% else %}use GitHub runners - "ubuntu-latest"{% endif %}{% raw %} @@ -69,7 +69,7 @@ jobs: name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}" needs: [nf-test-changes] if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} - runs-on: // {% endraw %}{% if is_nfcore %}use self-hosted runners + runs-on: #{% endraw %}{% if is_nfcore %} use self-hosted runners - runs-on=${{ github.run_id }}-nf-test - runner=4cpu-linux-x64{% else %}use GitHub runners - "ubuntu-latest"{% endif %}{% raw %} @@ -111,7 +111,7 @@ jobs: confirm-pass: needs: [nf-test] if: always() - runs-on: // {% endraw %}{% if is_nfcore %}use self-hosted runners + runs-on: {% endraw %}#{% if is_nfcore %} use self-hosted runners - runs-on=${{ github.run_id }}-confirm-pass - runner=2cpu-linux-x64{% else %}use GitHub runners - "ubuntu-latest"{% endif %}{% raw %} From 129858bd81af57f4c4add8f7c036043428af4e6e Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 2 Jun 2025 15:43:32 +0200 Subject: [PATCH 2/5] update changelog and bump version --- CHANGELOG.md | 6 ++++++ setup.py | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8f862b368a..9131ea6bd7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # nf-core/tools: Changelog +## [v3.3.1 - Tungsten Tamarin Patch](https://github.com/nf-core/tools/releases/tag/3.3.1) - [2025-06-02] + +### Template + +- Fix nf-test.yml file formatting ([#3601](https://github.com/nf-core/tools/pull/3601)) + ## [v3.3.0 - Tungsten Tamarin](https://github.com/nf-core/tools/releases/tag/3.3.0) - [2025-06-02] **Highlights** diff --git a/setup.py b/setup.py index b9414cdfd3..cfbcf96d8c 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "3.3.0" +version = "3.3.1" with open("README.md") as f: readme = f.read() From 286b6fe66f133bebdd6a0e84706d44b1e49ac637 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 2 Jun 2025 15:49:32 +0200 Subject: [PATCH 3/5] Update nf_core/pipeline-template/.github/workflows/nf-test.yml MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- nf_core/pipeline-template/.github/workflows/nf-test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml index eeba2ad132..f3f108a200 100644 --- a/nf_core/pipeline-template/.github/workflows/nf-test.yml +++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml @@ -71,7 +71,7 @@ jobs: if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }} runs-on: #{% endraw %}{% if is_nfcore %} use self-hosted runners - runs-on=${{ github.run_id }}-nf-test - - runner=4cpu-linux-x64{% else %}use GitHub runners + - runner=4cpu-linux-x64{% else %} use GitHub runners - "ubuntu-latest"{% endif %}{% raw %} strategy: fail-fast: false From ecbd5f5a382cafdcd170e689ec1c2a1f86e07cb5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 2 Jun 2025 15:51:25 +0200 Subject: [PATCH 4/5] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9131ea6bd7..1cacdee501 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ ### Template -- Fix nf-test.yml file formatting ([#3601](https://github.com/nf-core/tools/pull/3601)) +- Use correct comment symbol in `nf-test.yml` ([#3601](https://github.com/nf-core/tools/pull/3601)) ## [v3.3.0 - Tungsten Tamarin](https://github.com/nf-core/tools/releases/tag/3.3.0) - [2025-06-02] From c634d1b55f7a661695ed96cca7ecacf47ec02a3f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 2 Jun 2025 15:53:05 +0200 Subject: [PATCH 5/5] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- nf_core/pipeline-template/.github/workflows/nf-test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml index f3f108a200..a56df853f0 100644 --- a/nf_core/pipeline-template/.github/workflows/nf-test.yml +++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml @@ -36,7 +36,7 @@ jobs: name: nf-test-changes runs-on: #{% endraw %}{% if is_nfcore %} use self-hosted runners - runs-on=${{ github.run_id }}-nf-test-changes - - runner=4cpu-linux-x64{% else %}use GitHub runners + - runner=4cpu-linux-x64{% else %} use GitHub runners - "ubuntu-latest"{% endif %}{% raw %} outputs: shard: ${{ steps.set-shards.outputs.shard }} @@ -113,7 +113,7 @@ jobs: if: always() runs-on: {% endraw %}#{% if is_nfcore %} use self-hosted runners - runs-on=${{ github.run_id }}-confirm-pass - - runner=2cpu-linux-x64{% else %}use GitHub runners + - runner=2cpu-linux-x64{% else %} use GitHub runners - "ubuntu-latest"{% endif %}{% raw %} steps: - name: One or more tests failed