New sbwf bam_subsampledepth_samtools

[LouisLeNezet]

This PR introduce a new subworkflow that downsample alignment files to a given depth.

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    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
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[fellen31]

I don't really understand how this would be downsampling the reads in SAMTOOLS_VIEW, have you missed something?

[LouisLeNezet]

Hi @fellen31 I've effectively forgot to push my modification of SAMTOOLS_VIEW.

[SPPearce]

This looks good, but I'm not sure on the name.
This is downsampling to a mean depth, rather than a total number of reads, which would be another valid option on how to downsample.

[fellen31]

This looks a lot better to me, nice! Will let @SPPearce or someone else approve the naming though :)

[SPPearce]

Looks good to me, name approved on the subworkflows channel in the slack.

[SPPearce]

@LouisLeNezet , I think we're good to merge this in if you are happy.