[FEATURE] Adding bed output to bigWigAverageOverBed
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Description
Is your feature request related to a problem? Please describe
Hi,
I think the bigWigAverageOverBed command is also able to generate a bedoutput with a given argument that could be passed from config. See this
-bedOut=out.bed - Make output bed that is echo of input bed but with mean column appended
I understand with the current module it's not possible to capture this bed file, right? If there is a way to do this, could someone let me know how?
Describe the solution you'd like
Add an optional bed output in the bigWigAverageOverBed process module. I should be able to submit a PR for this if there's interest in the feature.
Describe alternatives you've considered
No response
Additional context
Tagging @jianhong as mantainer of the module.
Contributor guide
First steps
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Research direction
Locate the bigWigAverageOverBed module and its nf-test coverage, then inspect how the process currently exposes outputs. Use the documented -bedOut argument as the target behavior; done means an optional bed output can be requested and captures the command's generated bed file.
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
- 48/100