nf-core / nf-core/phageannotator
Running geNomad and COBRA fails because of altered FASTA sequence name
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bug
- Dominant language
- Nextflow
- Stars
- 19
- Forks
- 8
- PR merge metrics
- No merged PRs in 30d
Description
Description of the bug
In the geNomad summary, contigs with a prophage have a suffix added to its name. This results in COBRA unable to find the name in the original contig FASTA file.
Command used and terminal output
Relevant files
No response
System information
No response
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 geNomad-to-COBRA handoff described in the issue and trace where FASTA sequence names are transformed. The fix is complete when contig names with prophage annotations remain resolvable by COBRA against the original FASTA records.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100