Add flag to stop pipeline when bam + qc has been generated

[alkc]

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:

1. BAM realignment in the whambam bam service
2. QC-only runs of individual samples incomplete trios? Is this relevant?

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:

• Add params.alignment_only
• Add !params.alignment_only to processes that take dedup output as input
• Add !params.alignment_only to processes that take fetch_MTseqs output as input
• Clean out potentially unused channels, e.g. old chanjo bam.
  • chanjo_bam
  • yaml_bam
  • bam_nator