DO NOT MERGE update fasta_index_dna

[bhargava-morampalli]

PR checklist

Closes

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[SPPearce]

Several of your tests in the snapshot seem to be outputting the whole test work directory, which is then failing due to not being consistent.
I'm not sure why it is doing that though.
We often see similar behaviour when a file is created that ends in .gz but isn't actually gzipped (often empty files that are present in a stub), but I don't think that is happening here.
You also need to remove the pytest files and swap e.g. file(params.test_data['sarscov2']['genome']['genome_fasta'],checkIfExists:true) to be the newer params.modules_testdata_path` structure.

[SPPearce]

I can't see any obvious reason why nf-test would behave differently for the two bwa tools to snapaligner and bowtie.
I would suggest trying altering the output folder name/structure in one of the two bwa modules and see if that makes any difference (e.g. try tuple val(meta), path("bwa/") , emit: index, or tuple val(meta), path("foo") , emit: index, with changing the code itself to use foo).

[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