Fix inclusion of input bams in work directory

[anoronh4]

Staged input bam and bai in a subfolder using stageAs, in order to prevent the inputs from matching the wildcard in the bam output channel.

PR checklist

Closes #3504

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[nvnieuwk]

Inputs files are always excluded from the output glob pattern, so this shouldn't be a problem. You can also change the output to ${prefix}.bam instead if you want to be 100% certain that only the output BAM is in the output channel. Using stageAs should be seen as a last resort option, which isn't the case here :)

[anoronh4]

Inputs files are always excluded from the output glob pattern, so this shouldn't be a problem. You can also change the output to ${prefix}.bam instead if you want to be 100% certain that only the output BAM is in the output channel. Using stageAs should be seen as a last resort option, which isn't the case here :)

@nvnieuwk yea it's occurring to me that there is a problem, but not exactly what i thought. the bam isn't exactly going into the output channel. nonetheless, the file is being copied from the scratch directory instead of being cleaned up, and becoming a hard link. I will put this issue on the nextflow github and see what they say.

[anoronh4]

@nvnieuwk actually i found that someone else has posted the exact issue that fits here: nextflow-io/nextflow#3995 .

Since this issue has not been addressed by the nextflow team yet, should we fix the umitools/dedup module with this workaround? if so i'll merge the two PRs related to umitools/dedup (this one and #3506).