DO NOT MERGE update fasta_index_dna

[bhargava-morampalli]

PR checklist

Closes #7641

• [x] This comment contains a description of changes (with reason).
• [ ] If you've fixed a bug or added code that should be tested, add tests!
• [ ] If you've added a new tool - have you followed the module conventions in the contribution docs
• [ ] If necessary, include test data in your PR.
• [ ] Remove all TODO statements.
• [ ] Emit the versions.yml file.
• [ ] Follow the naming conventions.
• [ ] Follow the parameters requirements.
• [ ] Follow the input/output options guidelines.
• [ ] Add a resource label
• [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • [ ] nf-core modules test <MODULE> --profile docker
    • [ ] nf-core modules test <MODULE> --profile singularity
    • [ ] nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • [x] nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • [ ] nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • [ ] nf-core subworkflows test <SUBWORKFLOW> --profile conda

[SPPearce]

I think I've figured this out, just need to finish it off

[SPPearce]

I've updated this subworkflow, tests should hopefully now pass. However, it shouldn't be merged until a decision is made about what to do with the alt_liftover file, currently the bwa/mem modules do not output this into the bwa/ folder as is required for downstream use! i.e. the channel structure is now wrong.

[LouisLeNezet]

@SPPearce as per: https://nfcore.slack.com/archives/C043UU89KKQ/p1748441535247279 We can add an extra input to bwa mem to use the alt file as a separate channel as you suggested. The pytest files can also be definitely removed !

[SPPearce]

Replaced by #8962