diff --git a/CHANGELOG.md b/CHANGELOG.md index 8398b70e8c..11f15766ed 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -32,6 +32,7 @@ - Modified devcontainer permissions so that singularity can be run in Codespaces/VS Code devcontainers ([Commit a103f44](https://github.com/CarsonJM/tools/commit/a103f4484eca8c6d668e4653a4ed8d20faf1b41d)) - Update Gitpod profile resources to reflect base environment settings. - ([#747](https://github.com/nf-core/tools/issues/747)) Add to the template the code to dump the selected pipeline parameters into a json file. +- [#2161] Disable process selector warnings by default. ### Download diff --git a/nf_core/pipeline-template/.github/CONTRIBUTING.md b/nf_core/pipeline-template/.github/CONTRIBUTING.md index 6a1b9a9176..881ecbb022 100644 --- a/nf_core/pipeline-template/.github/CONTRIBUTING.md +++ b/nf_core/pipeline-template/.github/CONTRIBUTING.md @@ -31,6 +31,9 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests +You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to +receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. + When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. diff --git a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md index 0f81ebaa4c..4f01a97993 100644 --- a/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md +++ b/nf_core/pipeline-template/.github/PULL_REQUEST_TEMPLATE.md @@ -21,6 +21,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/{{ name }}/t {%- endif %} - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 31d6d90ccb..8c737b7a14 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -91,6 +91,7 @@ profiles { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' cleanup = false + nextflow.enable.configProcessNamesValidation = true } conda { conda.enabled = true @@ -216,6 +217,9 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Disable process selector warnings by default. Use debug profile to enable warnings. +nextflow.enable.configProcessNamesValidation = false + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true