From 43cea914c6df5725f90819fa6852dab61f557a1d Mon Sep 17 00:00:00 2001 From: znorgaard Date: Fri, 12 Jun 2026 15:26:56 -0700 Subject: [PATCH 1/2] fix: correct always-true lint condition and template doc typos - linting.yml: the non-release lint step used `base_ref != 'master' || base_ref != 'main'`, which is always true (a value can't equal both), so the non-release lint also ran on release PRs to main/master. Use `&&` so it runs only when the base is neither. - CONTRIBUTING.md: fix broken `[Lint](lint)` checklist link -> `#lint-tests` (matches the correct anchor used earlier in the same file); remove a duplicate "the the". - usage.md: remove stray leading space inside the Wave Nextflow-version code span (`` ` 24.03.0-edge` `` -> `` `24.03.0-edge` ``). Co-Authored-By: Claude Opus 4.8 (1M context) --- CHANGELOG.md | 1 + nf_core/pipeline-template/.github/workflows/linting.yml | 2 +- nf_core/pipeline-template/docs/CONTRIBUTING.md | 4 ++-- nf_core/pipeline-template/docs/usage.md | 2 +- 4 files changed, 5 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2e3af72c0f..90fc7b9f30 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,6 +31,7 @@ - add `process_low_memory` resource label to `base.config` ([#4264](https://github.com/nf-core/tools/pull/4264)) - fix dead link ([#4307](https://github.com/nf-core/tools/pull/4307)) - remove date placeholder from changelog title ([#4333](https://github.com/nf-core/tools/pull/4333)) +- correct always-true `nf-core pipelines lint` condition in the linting workflow and fix doc typos (broken `#lint-tests` anchor, duplicate word, stray code-span space) ([#XXXX](https://github.com/nf-core/tools/pull/XXXX)) #### Version updates diff --git a/nf_core/pipeline-template/.github/workflows/linting.yml b/nf_core/pipeline-template/.github/workflows/linting.yml index 05f710dce7..02e176a455 100644 --- a/nf_core/pipeline-template/.github/workflows/linting.yml +++ b/nf_core/pipeline-template/.github/workflows/linting.yml @@ -46,7 +46,7 @@ jobs: run: uv tool install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }} - name: Run nf-core pipelines lint - if: ${{ github.base_ref != 'master' || github.base_ref != 'main' }} + if: ${{ github.base_ref != 'master' && github.base_ref != 'main' }} env: GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/nf_core/pipeline-template/docs/CONTRIBUTING.md b/nf_core/pipeline-template/docs/CONTRIBUTING.md index 866c124543..981b29509e 100644 --- a/nf_core/pipeline-template/docs/CONTRIBUTING.md +++ b/nf_core/pipeline-template/docs/CONTRIBUTING.md @@ -144,7 +144,7 @@ Please also refer to the [pipeline-specific contribution guidelines](#pipeline-s - [ ] Perform local tests to validate that the new code works as expected. - [ ] If applicable, add a new test in the `tests` directory. - [ ] Update `usage.md`, `output.md`, and `citation.md` as appropriate. -- [ ] [Lint](lint) the code with nf-core/tools. +- [ ] [Lint](#lint-tests) the code with nf-core/tools. - [ ] Update any diagrams or pipeline images as necessary. {%- if multiqc %} - [ ] Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name cleanup, and module plots are in the appropriate order. @@ -184,7 +184,7 @@ Specify these with generic `withLabel:` selectors, so they can be shared across nf-core provides a set of standard labels that you should follow where possible, as seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/conf/base.config). These labels define resource defaults for single-core processes, modules that require a GPU, and different levels of multi-core configurations with increasing memory requirements. -Values assigned within these labels can be dynamically passed to a tool using the the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). +Values assigned within these labels can be dynamically passed to a tool using the `${task.cpus}` and `${task.memory}` Nextflow variables in the `script:` block of a module (see an example in the [modules repository](https://github.com/nf-core/modules/blob/bd1b6a40f55933d94b8c9ca94ec8c1ea0eaf4b82/modules/nf-core/samtools/bam2fq/main.nf#L30)). #### Nextflow version bumping diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md index a711f0d0a2..ca7e7748fd 100644 --- a/nf_core/pipeline-template/docs/usage.md +++ b/nf_core/pipeline-template/docs/usage.md @@ -165,7 +165,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `apptainer` - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) - `wave` - - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). + - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow `24.03.0-edge` or later). - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. From 0f26a20d62febaef97222ae6145461a0fd773700 Mon Sep 17 00:00:00 2001 From: znorgaard Date: Fri, 12 Jun 2026 15:36:58 -0700 Subject: [PATCH 2/2] docs: fill in PR number in changelog entry Co-Authored-By: Claude Opus 4.8 (1M context) --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 90fc7b9f30..5942c75913 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,7 +31,7 @@ - add `process_low_memory` resource label to `base.config` ([#4264](https://github.com/nf-core/tools/pull/4264)) - fix dead link ([#4307](https://github.com/nf-core/tools/pull/4307)) - remove date placeholder from changelog title ([#4333](https://github.com/nf-core/tools/pull/4333)) -- correct always-true `nf-core pipelines lint` condition in the linting workflow and fix doc typos (broken `#lint-tests` anchor, duplicate word, stray code-span space) ([#XXXX](https://github.com/nf-core/tools/pull/XXXX)) +- correct always-true `nf-core pipelines lint` condition in the linting workflow and fix doc typos (broken `#lint-tests` anchor, duplicate word, stray code-span space) ([#4324](https://github.com/nf-core/tools/pull/4324)) #### Version updates