From a5718f70e08a21e0baeb30ff620f2d93fa32db53 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 30 Aug 2024 16:11:06 +0200 Subject: [PATCH 1/3] test pipeline with conda and singularity on PRs to master --- nf_core/pipeline-template/.github/workflows/ci.yml | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml index 63fa99cec8..ade1b0c495 100644 --- a/nf_core/pipeline-template/.github/workflows/ci.yml +++ b/nf_core/pipeline-template/.github/workflows/ci.yml @@ -38,9 +38,21 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data + - name: Run pipeline with test data (docker) # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix run: | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results + + - name: Run pipeline with test data (singularity) + # TODO nf-core: You can customise CI pipeline run tests as required + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results + if: "{% raw %}${{ github.base_ref == 'master' }}{% endraw %}" + + - name: Run pipeline with test data (conda) + # TODO nf-core: You can customise CI pipeline run tests as required + run: | + nextflow run ${GITHUB_WORKSPACE} -profile test,conda --outdir ./results + if: "{% raw %}${{ github.base_ref == 'master' }}{% endraw %}" From 248b669ed7f8acffedfa3d9646d561508023a7d0 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 30 Aug 2024 16:12:28 +0200 Subject: [PATCH 2/3] add workflow_dispatch to pipeline ci test --- nf_core/pipeline-template/.github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/nf_core/pipeline-template/.github/workflows/ci.yml b/nf_core/pipeline-template/.github/workflows/ci.yml index ade1b0c495..685673de64 100644 --- a/nf_core/pipeline-template/.github/workflows/ci.yml +++ b/nf_core/pipeline-template/.github/workflows/ci.yml @@ -7,6 +7,7 @@ on: pull_request: release: types: [published] + workflow_dispatch: env: NXF_ANSI_LOG: false From 88f97357d6c0cb19ebfeee47cdc63ac2fba50e5f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 30 Aug 2024 16:14:12 +0200 Subject: [PATCH 3/3] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e198caa50..101b84c4ee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -36,6 +36,7 @@ - add option to exclude documentation from pipeline template ([#3130](https://github.com/nf-core/tools/pull/3130)) - add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133)) - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134)) +- test pipeline with conda and singularity on PRs to master ([#3149](https://github.com/nf-core/tools/pull/3149)) ### Linting