Write QC Generation workflow which should include:

[rhshah]

BAM QC: Inputs:

• BAM

• BED

  RUN:

• [x] Picard CollectMultipleMetrics
• [x] Picard CollectHSmetrics
• [x] Waltz PileupMetrics
• [x] Waltz CountReads

Collapsed FASTQ QC:

Input:

• Collapsed R1 FASTQ

• Collapsed R2 FASTQ

  Run

• [ ] BASH SCRIPT CWL

[murphycj2]

@ionox0 @rhshah for the second part, what is BASH SCRIPT CWL? is that a bash script somewhere in the access-pipeline repo?

[ionox0]

I believe that refers to the calculate_noise.sh and make_umi_qc_tables.sh scripts, which I am currently putting into the sequence_qc python package

[murphycj2]

PR: #108