From 7a3919436ab3b621c9493ed81db4ccaea56f7c36 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marius=20Bj=C3=B8rnstad?= Date: Mon, 16 Oct 2023 14:30:44 +0200 Subject: [PATCH] Add hint about debug profile --- src/content/docs/contributing/adding_pipelines.md | 3 +++ src/content/docs/contributing/contributing_to_pipelines.md | 3 +++ 2 files changed, 6 insertions(+) diff --git a/src/content/docs/contributing/adding_pipelines.md b/src/content/docs/contributing/adding_pipelines.md index 57ebbf23a7..130605e3b2 100644 --- a/src/content/docs/contributing/adding_pipelines.md +++ b/src/content/docs/contributing/adding_pipelines.md @@ -131,6 +131,9 @@ to make sure that your workflow passes all of the nf-core compatibility tests. The automated tests on Github Actions also run this, so you should get a notification from GitHub if something breaks. +When testing the pipeline you can add the `debug` profile (`-profile debug`) to the Nextflow command line, +to enable warnings about process selectors, show additional debug output and disable cleanup. + ## Running with test data Whilst the linting tests are good, they're not sufficient by themselves. diff --git a/src/content/docs/contributing/contributing_to_pipelines.md b/src/content/docs/contributing/contributing_to_pipelines.md index 521a018ed9..c59548251d 100644 --- a/src/content/docs/contributing/contributing_to_pipelines.md +++ b/src/content/docs/contributing/contributing_to_pipelines.md @@ -48,6 +48,9 @@ If you're new to working with git, you can view the [GitHub pull requests docume ## Testing +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.