add writing index option to samtools sort

[ljwharbers]

This adds the ability to include an index of choice using samtools sort. Currently it was only possible to use the ext.args = "--write-index" which will only output a .csi index. This adds a new val channel input that will output the selected bam/sam/cram index. If the channel is left empty '' no index will be written and the old behaviour is maintained.

This is the same as the use case in the latest version of samtools/view and minimap2/align and will reduce a lot of unecessary SAMTOOLS_SORT into SAMTOOLS_INDEX processes.

Due to many modules/subworkflows use samtools sort (for instance in BAM_SORT_STATS_SAMTOOLS), other tests are also updated to include an empty third input channel to maintain the old behaviour.

Optionally BAM_SORT_STATS_SAMTOOLS can also be updated to now entirely skip SAMTOOLS_INDEX and simply directly write the bai index within SAMTOOLS_SORT

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[ljwharbers]

@nf-core-bot update gpu snapshot path: subworkflows/nf-core/fastq_align_dedup_bwameth

[fellen31]

Looks good, just one thing.

[fellen31]

I would add a check for this here and in the stub.

if (index_format) {
        if (!index_format.matches('bai|csi|crai')) {
            error "Index format not one of bai, csi, crai."
        } else if (extension == "sam") {
            error "Indexing not compatible with SAM output"
        }
    }

Since technically, index_format can be anything, but we only have outputs for bai, crai, csi (I'm team emit: index, but that's another discussion).

[ljwharbers]

I agree, I would also prefer a simple emit: index option. Either way, I've added the check like this.

[ljwharbers]

@fellen31 Thanks for reviewing! So it's all good to merge once checks are complete or does it need approval of anyone else first still?

[fellen31]

I say good to merge!

Perhaps some extra care could be taken since changing samtools sort might affect many pipelines, but we had the discussion already for samtools view and came to a conclusion (#4326), and this implementation is exactly the same.