This is a feature request for a flag to wgs-hg38 that terminates the pipeline execution after the BAM and associated sequencing QC data have been completed.
This is useful for:
BAM realignment in the whambam bam service
QC-only runs of individual samples incomplete trios? Is this relevant?
This is a feature request for a flag to wgs-hg38 that terminates the pipeline execution after the BAM and associated sequencing QC data have been completed.
This is useful for:
Mostly number #1 is of interest.
This issue is related to ongoing work for https://github.com/Clinical-Genomics-Lund/bam_service/issues/1
TODO:
params.alignment_only
!params.alignment_only
to processes that takededup
output as input!params.alignment_only
to processes that takefetch_MTseqs
output as input