From 76c3753ab0c89063348d5b1771d9ffed1b3fc832 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 13 Aug 2024 13:38:05 +0200 Subject: [PATCH 1/6] rename tests --- .github/workflows/ci.yml | 2 +- .../{main_pipeline_alevin.test => main_pipeline_alevin.nf.test} | 0 ...eline_alevin.test.snap => main_pipeline_alevin.nf.test.snap} | 0 ...ipeline_cellranger.test => main_pipeline_cellranger.nf.test} | 0 ...llranger.test.snap => main_pipeline_cellranger.nf.test.snap} | 0 ...llrangermulti.test => main_pipeline_cellrangermulti.nf.test} | 0 ...lti.test.snap => main_pipeline_cellrangermulti.nf.test.snap} | 0 ...in_pipeline_kallisto.test => main_pipeline_kallisto.nf.test} | 0 ...e_kallisto.test.snap => main_pipeline_kallisto.nf.test.snap} | 0 tests/{main_pipeline_star.test => main_pipeline_star.nf.test} | 0 ..._pipeline_star.test.snap => main_pipeline_star.nf.test.snap} | 0 11 files changed, 1 insertion(+), 1 deletion(-) rename tests/{main_pipeline_alevin.test => main_pipeline_alevin.nf.test} (100%) rename tests/{main_pipeline_alevin.test.snap => main_pipeline_alevin.nf.test.snap} (100%) rename tests/{main_pipeline_cellranger.test => main_pipeline_cellranger.nf.test} (100%) rename tests/{main_pipeline_cellranger.test.snap => main_pipeline_cellranger.nf.test.snap} (100%) rename tests/{main_pipeline_cellrangermulti.test => main_pipeline_cellrangermulti.nf.test} (100%) rename tests/{main_pipeline_cellrangermulti.test.snap => main_pipeline_cellrangermulti.nf.test.snap} (100%) rename tests/{main_pipeline_kallisto.test => main_pipeline_kallisto.nf.test} (100%) rename tests/{main_pipeline_kallisto.test.snap => main_pipeline_kallisto.nf.test.snap} (100%) rename tests/{main_pipeline_star.test => main_pipeline_star.nf.test} (100%) rename tests/{main_pipeline_star.test.snap => main_pipeline_star.nf.test.snap} (100%) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7035fe9c..28b26130 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -64,7 +64,7 @@ jobs: - name: Run nf-test run: | - nf-test test tests/main_pipeline_${{ matrix.profile }}.test --junitxml=test.xml + nf-test test tests/main_pipeline_${{ matrix.profile }}.nf.test --junitxml=test.xml - name: Output log on failure if: failure() diff --git a/tests/main_pipeline_alevin.test b/tests/main_pipeline_alevin.nf.test similarity index 100% rename from tests/main_pipeline_alevin.test rename to tests/main_pipeline_alevin.nf.test diff --git a/tests/main_pipeline_alevin.test.snap b/tests/main_pipeline_alevin.nf.test.snap similarity index 100% rename from tests/main_pipeline_alevin.test.snap rename to tests/main_pipeline_alevin.nf.test.snap diff --git a/tests/main_pipeline_cellranger.test b/tests/main_pipeline_cellranger.nf.test similarity index 100% rename from tests/main_pipeline_cellranger.test rename to tests/main_pipeline_cellranger.nf.test diff --git a/tests/main_pipeline_cellranger.test.snap b/tests/main_pipeline_cellranger.nf.test.snap similarity index 100% rename from tests/main_pipeline_cellranger.test.snap rename to tests/main_pipeline_cellranger.nf.test.snap diff --git a/tests/main_pipeline_cellrangermulti.test b/tests/main_pipeline_cellrangermulti.nf.test similarity index 100% rename from tests/main_pipeline_cellrangermulti.test rename to tests/main_pipeline_cellrangermulti.nf.test diff --git a/tests/main_pipeline_cellrangermulti.test.snap b/tests/main_pipeline_cellrangermulti.nf.test.snap similarity index 100% rename from tests/main_pipeline_cellrangermulti.test.snap rename to tests/main_pipeline_cellrangermulti.nf.test.snap diff --git a/tests/main_pipeline_kallisto.test b/tests/main_pipeline_kallisto.nf.test similarity index 100% rename from tests/main_pipeline_kallisto.test rename to tests/main_pipeline_kallisto.nf.test diff --git a/tests/main_pipeline_kallisto.test.snap b/tests/main_pipeline_kallisto.nf.test.snap similarity index 100% rename from tests/main_pipeline_kallisto.test.snap rename to tests/main_pipeline_kallisto.nf.test.snap diff --git a/tests/main_pipeline_star.test b/tests/main_pipeline_star.nf.test similarity index 100% rename from tests/main_pipeline_star.test rename to tests/main_pipeline_star.nf.test diff --git a/tests/main_pipeline_star.test.snap b/tests/main_pipeline_star.nf.test.snap similarity index 100% rename from tests/main_pipeline_star.test.snap rename to tests/main_pipeline_star.nf.test.snap From 0ce64b1f7c108f3205f1f76e2a7a9afc03954313 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 13 Aug 2024 14:10:55 +0200 Subject: [PATCH 2/6] Update nf-test CI and nf-validation plugin --- .github/workflows/ci.yml | 33 +++++++++++++++++---------------- nextflow.config | 2 +- 2 files changed, 18 insertions(+), 17 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 28b26130..64e3920a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -42,29 +42,30 @@ jobs: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - - name: Install Nextflow - uses: nf-core/setup-nextflow@v2 + - uses: actions/setup-python@v4 with: - version: "${{ matrix.NXF_VER }}" + python-version: "3.11" + architecture: "x64" + + - name: Install pdiff to see diff between nf-test snapshots + run: | + python -m pip install --upgrade pip + pip install pdiff - - name: Cache nf-test installation - id: cache-software - uses: actions/cache@v3 + - uses: nf-core/setup-nextflow@v2 with: - path: | - /usr/local/bin/nf-test - /home/runner/.nf-test/nf-test.jar - key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest + version: "${{ matrix.NXF_VER }}" - - name: Install nf-test - if: steps.cache-software.outputs.cache-hit != 'true' - run: | - wget -qO- https://code.askimed.com/install/nf-test | bash - sudo mv nf-test /usr/local/bin/ + - uses: nf-core/setup-nf-test@v1 + with: + version: ${{ env.NFT_VER }} - name: Run nf-test run: | - nf-test test tests/main_pipeline_${{ matrix.profile }}.nf.test --junitxml=test.xml + nf-test test \ + --ci \ + --junitxml=test.xml \ + tests/main_pipeline_${{ matrix.profile }}.nf.test - name: Output log on failure if: failure() diff --git a/nextflow.config b/nextflow.config index 0e5c3dcf..3c807cdf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -249,7 +249,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation@1.1.4' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Load igenomes.config if required From 7adc979eba03c4e03e6f3b52d900bce3c398c65f Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 13 Aug 2024 14:16:28 +0200 Subject: [PATCH 3/6] Fix env vars --- .github/workflows/ci.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 64e3920a..4b3c26a0 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -16,7 +16,10 @@ on: env: NXF_ANSI_LOG: false - NFTEST_VER: "0.8.1" + NFT_VER: "0.9.0" + NFT_WORKDIR: "~" + NFT_DIFF: "pdiff" + NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" From 9a3109031a1a2c8a2a8d539c29a07e971c88729f Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 13 Aug 2024 15:19:40 +0200 Subject: [PATCH 4/6] Revert "Re-enable schema linting" This reverts commit 6da07872a8832902f78af7315d9e0411860bb465. --- .nf-core.yml | 3 +++ nextflow.config | 5 +++++ 2 files changed, 8 insertions(+) diff --git a/.nf-core.yml b/.nf-core.yml index 7c377491..73506c0f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -6,3 +6,6 @@ lint: - .github/ISSUE_TEMPLATE/bug_report.yml files_exist: - lib/Utils.groovy + # TODO This is because of an issue with the monochromeLogs parameter + # See nextflow.config for details + schema_params: False diff --git a/nextflow.config b/nextflow.config index 3c807cdf..e1b608d2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -116,6 +116,11 @@ params { validationShowHiddenParams = false validate_params = true + // TODO temporary workaround a warning + // not used anywhere and should not be necessary anymore after a nf-validation plugin update + // TODO when removing this, also remove the ignored lint check from .nf-core.yml + monochromeLogs = null + } // Load base.config by default for all pipelines From 7da25ee23059ab0424b925c11c40588a049231f8 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 13 Aug 2024 15:39:42 +0200 Subject: [PATCH 5/6] Update CHANGELOG --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ccf60d1c..42bd7626 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v2.7.1 - 2024-08-13 -- Re-enable linting check for nextflow schema ([#354](https://github.com/nf-core/scrnaseq/pull/354)) +- Fix that tests have not been executed with nf-test v0.9 - Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348)) - Fix issues with predefined STAR index ([#350](https://github.com/nf-core/scrnaseq/pull/350)) - Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351)) From b1ef5bb53bb6f4deb362101c014c78ccea5ddfe7 Mon Sep 17 00:00:00 2001 From: Gregor Sturm Date: Tue, 13 Aug 2024 16:19:00 +0200 Subject: [PATCH 6/6] Update CHANGELOG.md Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 42bd7626..fd1b6e41 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v2.7.1 - 2024-08-13 -- Fix that tests have not been executed with nf-test v0.9 +- Fix that tests have not been executed with nf-test v0.9 ([#359](https://github.com/nf-core/scrnaseq/pull/359)) - Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348)) - Fix issues with predefined STAR index ([#350](https://github.com/nf-core/scrnaseq/pull/350)) - Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351))