diff --git a/docs/lint_errors.md b/docs/lint_errors.md index 1caf8c203c..dc84477354 100644 --- a/docs/lint_errors.md +++ b/docs/lint_errors.md @@ -100,16 +100,6 @@ These tests look at `process.container` and `$GITHUB_REF` only if they are set. * Container tag / `$GITHUB_REF` must contain only numbers and dots * Tags and `$GITHUB_REF` must all match one another -## Error #10 - Template TODO statement found ## {#10} - -The nf-core workflow template contains a number of comment lines with the following format: - -```groovy -// TODO nf-core: Make some kind of change to the workflow here -``` - -This lint test runs through all files in the pipeline and searches for these lines. - ## Error #14 - Pipeline schema syntax ## {#14} Pipelines should have a `nextflow_schema.json` file that describes the different pipeline parameters (eg. `params.something`, `--something`). diff --git a/nf_core/lint/actions_lint.py b/nf_core/lint/actions_lint.py index c3a18d337f..442bd9ad64 100644 --- a/nf_core/lint/actions_lint.py +++ b/nf_core/lint/actions_lint.py @@ -52,7 +52,7 @@ def actions_lint(self): steps: - run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml") - .. note:: These are minimal examples of the commands and YAML structure and are not complete + .. warning:: These are minimal examples of the commands and YAML structure and are not complete enough to be copied into the workflow file. """ passed = [] diff --git a/nf_core/lint/conda_dockerfile.py b/nf_core/lint/conda_dockerfile.py index 5b9f21a024..838493be71 100644 --- a/nf_core/lint/conda_dockerfile.py +++ b/nf_core/lint/conda_dockerfile.py @@ -34,7 +34,7 @@ def conda_dockerfile(self): * The linting tool compares the tag against the currently installed version of tools. * This line is not checked if running a development version of nf-core/tools. - .. seealso:: Additional lines and different metadata can be added to the ``Dockerfile`` + .. tip:: Additional lines and different metadata can be added to the ``Dockerfile`` without causing this lint test to fail. """ diff --git a/nf_core/lint/pipeline_todos.py b/nf_core/lint/pipeline_todos.py index 2512fcad32..c5cb907658 100644 --- a/nf_core/lint/pipeline_todos.py +++ b/nf_core/lint/pipeline_todos.py @@ -6,7 +6,29 @@ def pipeline_todos(self): - """ Go through all template files looking for the string 'TODO nf-core:' """ + """Check for nf-core *TODO* lines. + + The nf-core workflow template contains a number of comment lines to help developers + of new pipelines know where they need to edit files and add content. + They typically have the following format: + + .. code-block:: groovy + + // TODO nf-core: Make some kind of change to the workflow here + + ..or in markdown: + + .. code-block:: html + + + + This lint test runs through all files in the pipeline and searches for these lines. + If any are found they will throw a warning. + + .. tip:: Note that many GUI code editors have plugins to list all instances of *TODO* + in a given project directory. This is a very quick and convenient way to get + started on your pipeline! + """ passed = [] warned = [] failed = []