parabricks/fq2bam needs the fasta in the same folder as the BWAIndex
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Description
This leads to troubles when running on a cluster because a simple symlinking logic does not work there. However we want to move away from copying files which is not effective.
@gburnett-nvidia can you bring this up again with your team? Because we need fq2bam to be able to handle the reference differently. Maybe two command-line flags? One for fasta and one for the index?
We can update the module as soon as that works :)
See #9229 for the reverting to copying.
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 reviewing the current fq2bam module behavior and issue #9229 to understand the reverted copying approach. Confirm with the Parabricks team whether separate FASTA and BWA index inputs will be supported; done means the module can use that support without relying on same-folder symlinks or ineffective file copying.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, tooling
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100