nf-core / nf-core/pairgenomealign
Reduce `last/split` diff
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enhancement
- Dominant language
- Nextflow
- Stars
- 12
- Forks
- 5
- Avg merge
- 1d 10h
- Merged PRs (30d)
- 6
Description
Description of feature
- The
maf_to_matrix.pyscript should be submitted upstream, as it is a fork ofmaf-convert. - As noted by @tm4zza in https://github.com/nf-core/pairgenomealign/pull/151, the named pipe should be cleaned after use, and the
waitcommand should check the exit status (wait "$matrix_pid" || exit 1)
All of this should be done by the original last/split module itself instead of patching it.
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
Read the maf_to_matrix.py script and the original last/split module, using pull request #151 for context on the named-pipe cleanup and wait exit-status behavior. Update the original module so these changes are handled there rather than by a patch, and ensure maf_to_matrix.py is suitable for upstream submission.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Active
- Clarity
- Mostly clear
- Newbie friendliness
- 58/100