Add 'ext capture_logs: false' to remaining processes

[sorelfitzgibbon]

This is the same as uclahs-cds/pipeline-Nextflow-module#42, just covering a few last processes.

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Tested with pipeline-call-sSNV #314

[yashpatel6]

Looks good!

[nwiltsie]

Looks good! I confirmed that each process with the directive has an existing publishDir rule.