linting fails to execute if "----" present in module patch diff file
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- Dominant language
- Python
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Description
Description of the bug
Linting will fail to run if "----" is present in a module patch diff file.
In an nf-core pipeline that currently passes linting add one of the latest samtools modules.
nf-core modules install samtools/dict
Modify the environment.yaml file to use a name: and remove the schema reference, because without non-unique conda environments currently break nextflow (until the next release at least). https://github.com/nextflow-io/nextflow/pull/5489
name: samtools_dict
channels:
- conda-forge
- bioconda
dependencies:
- bioconda::htslib=1.21
- bioconda::samtools=1.21
Linting should still complete successfully at this point.
nf-core pipelines lint
Be responsible, document your patch! Run
nf-core modules patch samtools/dict
Now run linting again.
nf-core pipelines lint
ERROR not enough values to unpack (expected 2, got 1)
If you remove the "----" line from the diff file, linting will pass again.
Command used and terminal output
System information
Nextflow version: 24.04.4
Hardware: Desktop
Executor: NA
OS: macOS
nf-core/tools version: 3.0.2
python version: 3.12
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the failure by installing samtools/dict, editing environment.yaml, running nf-core modules patch samtools/dict, and then running nf-core pipelines lint. Start by tracing how the module patch diff is parsed, especially the "----" line; done means linting completes successfully without removing that line.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 52/100