Compress FASTA files with contigs and scaffolds using bgzip instead of gzip, to enable file indexing
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enhancement
- Dominant language
- Nextflow
- Stars
- 321
- Forks
- 156
- Avg merge
- 12h 59m
- Merged PRs (30d)
- 5
Description
Description of feature
Certain downstream analysis tools expect the FASTA files with contigs and scaffolds to be compressed with bgzip instead of gzip, for file indexing purposes. To save time with decompressing and recompressing, it would be helpful if the MEGAHIT and SPAdes modules would directly compress their outputs with bgzip instead of gzip.
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
Inspect the MEGAHIT and SPAdes modules and their output-compression steps first. Confirm how the current gzip handling is wired, then verify that contig and scaffold outputs use bgzip and are suitable for file indexing.
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
- 35/100