MAKE_GENE_BED making 0kb .bed files
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- Nextflow
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Description
Hi @drpatelh not sure if notifications work for "closed" issue threads. sorry if they do. I was hoping I could re-open this issue as I am still experiencing it with the latest DSL2 version. Cheers!
Hi @hcliedtke ! Thanks for reporting and apologies for the delay in responding! We are about to release a much updated version of the pipeline that has been completely refactored to be written in Nextflow DSL2. When this is released, it would be great if you can let us know if the problem still persists. I will close this issue for now.
For faster, real-time help for these sorts of things please join the #atacseq channel on the nf-core Slack workspace. You can join via the link below:
https://nf-co.re/join
Originally posted by @drpatelh in https://github.com/nf-core/atacseq/issues/170#issuecomment-1319926079
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 by reproducing the reported behavior with the latest DSL2 version and trace the MAKE_GENE_BED process that produces the .bed output. Done means the pipeline no longer creates 0kb .bed files for the affected input; the issue does not name a test or source file to run first.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100