Update salmon quant arguments - Githubissues

viash-hub / biobox

🌱📦 A collection of bioinformatics tools for working with sequence data.

https://web.viash-hub.dev/package/biobox

MIT License

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Update salmon quant arguments #57

Closed sainirmayi closed 5 months ago

sainirmayi commented 5 months ago

Description

Make --index an optional argument.
Change --write_mappings to boolean_true argument type.
Add output argument --mappings_sam that should be used with the --write_mappings argument to output alignments in SAM format

Issue ticket number

Closes #xxxx

Checklist before requesting a review

[x] I have performed a self-review of my code
[ ] Conforms to the Contributing guidelines
[ ] Proposed changes are described in the CHANGELOG.md
[x] I have tested my code with viash ns test --parallel -q <name or namespace>
Check the correct box. Does this PR contain:
- [ ] Breaking changes
- [ ] New functionality
- [ ] Major changes
- [ ] Minor changes
- [ ] Documentation
- [x] Bug fixes