[FEATURE] use `arity` in freebayes module to allow more than two input files
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- Nextflow
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Description
Is your feature request related to a problem? Please describe
BAM input handling in the current nf-code/freebayes module allows for specification of 1 or 2 bam input files (using input_1, input_1_index, input_2 and input_2_index path inputs).
However, this is not a limitation of freebayes, and furthermore nextflow allows path inputs to contain an arbitrary number of individual paths.
Describe the solution you'd like
- specify
alignmentandalignment_indexas path inputs with arity1..* - provide these inputs to freebayes
Describe alternatives you've considered
No response
Additional context
No response
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
Locate the nf-code/freebayes module and inspect how input_1, input_1_index, input_2, and input_2_index are currently declared and passed to freebayes. Replace that interface with alignment and alignment_index path inputs using the requested arity, then verify that one or more BAM inputs can be provided successfully.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100