Peddy can no longer be run without providing sites argument
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Description
Have you checked the docs?
Description of the bug
It looks like the Peddy module in nf-core has been updated to allow an optional sites argument.
The current way it is implemented makes it impossible to run Peddy without the sites argument. I am running into this error when running the nf-core pipeline Tomte. No parameters have changed from when I last updated the pipeline ~0.5 years ago.
Here is the input part.
Current (previously working) Tomte usage:
PEDDY (
ch_vcf_tbi,
ch_pedfile
)
Command used and terminal output
The crash message:
Process `TOMTE:PEDDY` declares 3 inputs but was called with 2 arguments
-- Check script '/fs1/jakob/src/nisse/tomte/workflows/tomte.nf' at line: 281 or see '.nextflow.log' file for more details
Relevant files
No response
System information
Nextflow version 25.10.0
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
Start with modules/nf-core/peddy/main.nf at the linked input declaration, then compare it with the Tomte call in workflows/tomte.nf around lines 280–283. Reproduce the two-argument invocation and inspect how the sites input is declared. Done means Peddy can be called without sites while still accepting it when provided.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, tooling
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 52/100