Fja readlength dev

[frankambrosio3]

TheiaProk now outputs readlength to the data table in order to satisfy requests from PNI.

• It now outputs r1, r2, and combined raw mean quality scores and read lengths to the Terra data table
• It also outputs the combined clean mean quality scores and read lengths, but does not show the individual r1 and r2 values to avoid column creep

TheiaProk Illumina PE output columns:

r1_mean_q_raw r2_mean_q_raw combined_mean_q_raw combined_mean_q_clean r1_mean_readlength_raw r2_mean_readlength_raw combined_mean_readlength_raw combined_mean_readlength_clean

TheiaProk Illumina SE output columns:

r1_mean_q_raw r1_mean_q_clean r1_mean_readlength_raw r1_mean_readlength_clean

This PR also adds the clean mean quality scores and readlengths to the qc_check task

[michellescribner]

Tested successfully

https://app.terra.bio/#workspaces/theiagen-validations/Theiagen_Scribner_Sandbox/job_history/69c40459-553c-4502-9425-ab3e4f64d044

378a70b4-2fa8-4fdb-b039-c60f24342b0b

[frankambrosio3]

pni_qc_check_table.txt qc check table (this is a tsv saved with a txt file ending)

[kevinlibuit]

PR looks solid! Thanks for getting this together to ensure we have more alignment with PNI QC standards.

No need to change things now, but if we get more requests to add potential metrics to measure against (e.g. r1_mean_q_clean in this PR), it seems like we're reaching a point where it will make more sense for us to write out a function as to consolidate any redundancy in that block and ease readability of the code.

Running a final test run for sanity's sake--I'm using the complete_qc_check_table.tsv file I saw in @michellescribner's sandbox.

I can merge things pending a successful run.

[michellescribner]

No need to change things now, but if we get more requests to add potential metrics to measure against (e.g. r1_mean_q_clean in this PR), it seems like we're reaching a point where it will make more sense for us to write out a function as to consolidate any redundancy in that block and ease readability of the code.

I completely agree! I will make that change next time we need to modify the task or earlier