feat: make FASTQ analysis optional

[adthrasher]

This makes the FASTQ portion of the QC pipeline optional. The default remains to run, but this allows a user to disable the analysis that depends on FASTQ files.

Also contains an off-topic change to add exceptions for EmptyOutputs to tasks with no expected outputs, since that rule was added to Sprocket. This is now in #317.

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[adthrasher]

Fix for GATK4 tests is in #282

[a-frantz]

as discussed over DM, the comments I request be deleted miss the mark. The fact they match the task default is a coincidence; the inputs have reason to be specified here at the workflow level.

Even though specifying here is technically redundant with relying on the default task values, I'd rather explicitly specify them here with the reasoning. Respecifying here at the workflow level is also a safeguard against the default switching out from under us

[a-frantz]

a take it or leave it doc suggestion, and another less confident thought I had about potential QC docs (tangent from this PR)