Change output directory and file names for bwa index

[pmoris]

• Changes the output directory's name from bwa to ${prefix}.
• Makes prefix default to meta.id instead of fasta.baseName.
• Add suffix and default it to fasta.baseName.
• Changes output filenames to ${suffix} .{amb,ann,bwt,pac,sa}

This improves the following situations:

1. When index files for multiple references are processed simultaneously in a single process (e.g. fastq screen), there are no longer identically named bwa directories being staged (-> could be avoided by using stageAs in the process input). 2) Makes it easier to publish the resulting output directories when processing multiple reference genomes sequentially (otherwise the bwa dirs would overwrite each other; this required adaptations in modules.config to avoid like: path: { "${params.outdir}/reference/${meta.id}" }).

See discussion here: https://nfcore.slack.com/archives/CJRH30T6V/p1770372215776389

A previous fix was proposed, but never merged: #7793

Two final considerations to make:

1. the current fix keeps things similar for downstream processes (i.e. the actual index files are still named the same as the input fasta file via fasta.baseName), but perhaps it could also be useful to do things the other way around: set the filename based on prefix/meta.id, so that it becomes possible to rename the files.
2. I resorted to repeating the task.prefix / meta.id to capture the output directory. If there's a tidier solution for this, I'm all ears.

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[pmoris]

I think this PR is more or less ready to be merged now, but as mentioned in Slack, the linter keeps failing. However, it was (at least locally) also failing for me on the master commit I started from (eb19663), and also on the current most recent commit (b94c791).

How should we proceed here?

╭─ [✗] 2 Module Tests Failed ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│              ╷                                    ╷                                                                                                                                                                   │
│ Module name  │ File path                          │ Test message                                                                                                                                                      │
│╶─────────────┼────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│
│ bwa/index    │ modules/nf-core/bwa/index/meta.yml │ correct_meta_outputs: Module meta.yml does not match main.nf. Outputs should contain: {'index': [['meta', 'bwa']], 'versions_bwa': [['${task.process}', 'bwa',    │
│              │                                    │ 'bwa 2>&1 | sed -n "s/^Version: //p']]} Run nf-core modules lint --fix to update the meta.yml file.                                                               │
│ bwa/index    │ modules/nf-core/bwa/index/meta.yml │ correct_meta_topics: Module meta.yml does not match main.nf. Topics should contain: {'versions': [['${task.process}', 'bwa', 'bwa 2>&1 | sed -n "s/^Version:      │
│              │                                    │ //p']]} Run nf-core modules lint --fix to update the meta.yml file.                                                                                               │
│              ╵                                    ╵                                                                                                                                                                   │
╰───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────