BWA_MEM silently receives 0 tasks when BWA index is built from FASTA (no pre-built index provided)
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bug
- Dominant language
- Nextflow
- Stars
- 230
- Forks
- 142
- Avg merge
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- Merged PRs (30d)
- 1
Description
Description of the bug
See this slack thread
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
The issue names the BWA_MEM workflow step but provides no relevant files, command, terminal output, or tests. Start by tracing how BWA_MEM receives inputs when an index is built from FASTA, then reproduce the zero-task behavior and verify that this input path schedules the expected tasks.
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
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 38/100