Samtools mpileup input update

[Krannich479]

PR checklist

Closes #9802

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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---

An extensive description of why I believe a new input section is necessary can be found in #9802 .

[Krannich479]

With commit 59c4331 :

• the input rolled back to the previous original format, just the index added to the tuple
• samtools version rolled back to 1.22.1 s.t. it matches the other modules again
• minor documentation fixes

[matthdsm]

fasta will also be required when using cram inputs, but that's implied and known when using cram data I guess

[matthdsm]

LGTM!
Thanks for wading through all the input

[Krannich479]

Thank you for all your valuable feedback!

[Krannich479]

I leave this here for documentation:
The way I parallelized SAMTOOLS_MPILEUP across chromosomes now is by passing the chromosome identifier to -r via the meta map.

    withName: 'SAMTOOLS_MPILEUP' {
        ext.args    = { "-r ${meta.region}" }
        ext.prefix  = { "${meta.id}.${meta.region}" }
    }