nf-core / nf-core/modules

[FEATURE] use `arity` in freebayes module to allow more than two input files

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Dominant language
Nextflow
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Merged PRs (30d)
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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 alignment and alignment_index as path inputs with arity 1..*
  • provide these inputs to freebayes
Describe alternatives you've considered

No response

Additional context

No response

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First steps

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  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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