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:

• [x] Add params.alignment_only
• [x] 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