Issue processing input data without read group info

[leahkemp]

Pipeface version: v0.1.1
Nextflow version: 24.04.1

Error message in nextflow:

ERROR ~ Error executing process > 'clair3 (1)'

But the error comes upstream from minimap2

Error message in Minimap2 log:

ERROR ~ Error executing process > 'clair3 (1)'

Caused by:
  Missing output file(s) `clair3.snp_indel.g.vcf.gz` expected by process `clair3 (1)`

I think this error comes from utilising the -R flag in Minimap2, when the input uBAM doesn't have read group info (@RG tag)

[leahkemp]

One way I'm looking at resolving this issue is by using deepvariant directly, instead of running deepvariant through clara parabricks. deepvariant looks to have a --sample_name flag (where clara parabricks doesn't expose this flag). So far I've been hamstring into modifying the @RG tags in the in the aligned BAM with samtools addreplacerg or during alignment with the -R flag in minimap2. But I think running deepvariant directly and using it's --sample_name flag will allow me to avoid this bug as well as any modification to the @RG tags, which is probably ideal. This potential fix could also resolve the related issue #8.