Port bedtools_genomecov from local to nf-core module
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Description
Description of feature
Description
Currently, the bedtools_genomecov module is implemented as a local module. There is however an nf-core module for it https://nf-co.re/modules/bedtools_genomecov. The local module should probably be ported to the nf-core module to ensure maintenance and allow users to set parameter space using ext.args, instead of relying on hard coded parameters for every execution, for example --bg / --bga (as described in https://github.com/nf-core/chipseq/issues/468)
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/local/bedtools_genomecov.nf and compare it with the nf-core bedtools_genomecov module linked in the issue. Check how the pipeline currently invokes the local module and review issue #468 for the --bg/--bga parameter context. Done means the local implementation is ported to the nf-core module and parameter selection can use ext.args.
Written by the indexing model from the issue text.
Assessment
- Domain
- data-engineering, tooling
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100