Add error/status codes to combo decontam task and main variant caller task

[aofarrel]

Adds task-level outputs that will return a status code for a given sample. This status code can be saved to a Terra data table, allowing someone to see at a glance why their sample failed (or if it passed).

Decontaminate task now can return:

• DECONTAMINATION_MAP_READS_TIMEOUT
• DECONTAMINATION_MAP_READS_KILLED
• DECONTAMINATION_MAP_READS_UNKNOWN_ERROR
• DECONTAMINATION_RM_CONTAM_TIMEOUT
• DECONTAMINATION_RM_CONTAM_KILLED
• DECONTAMINATION_RM_CONTAM_UNKNOWN_ERROR
• PASS

Variant caller now can return:

• VARIANT_CALLING_TIMEOUT
• VARIANT_CALLING_KILLED
• VARIANT_CALLING_ADJUDICATION_FAILURE
• VARIANT_CALLING_UNKNOWN_ERROR
• PASS

The adjudication failure represents porting a check from an older version of the variant caller. That check will look at Cortex logs for a warning that, in my experience, indicates that a file was too small for Cortex but not small enough for minimap2. My understanding is that the actual error occurs in minos, so I'm calling this a minos error instead of a Cortex one.

This does not include any of the fancy calculus needed to get these error codes on a data table. That's the purview of myco_raw.

[aofarrel]

It should be admitted that the event that triggers VARIANT_CALLING_ADJUDICATION_FAILURE has not been tested in a while. Ideally, a sample that triggers it should be found before merging, but it was a relatively rare situation to begin with so that might not be feasible... perhaps it can be forced by downsampling?

[aofarrel]

Having trouble replicating adjudication failure on a downsampled test fastq even after skipping earlyQC, but I did manage to get VARIANT_CALLING_UNKNOWN_ERROR when the variant caller threw Failed to parse the output of get_auto_cleaning_cutoff.R

I think it's high time to merge this, since the change on this particular repo is very small.