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For generate-SQC-BAM I propose to use plot-bamstats which is part of the SAMtools package to create sample level BAM QC plots from the SAMtools stats output. Here are the default plots for a single PCAWG sample: plots-bamstats-pcawg63.pdf.
This requires adding gnuplot to the SAMtools docker, which Claude estimated would only add 5-10 MB out of 100-200 MB for SAMtools alone.
For the generate-CQC-BAM I propose using the scripts currently in tool-QC-script to generate these cohort level plots from both the SAMtools stats and Picard CollectWGSmetrics outputs. plots-cohort-pcawg63.pdf
In both cases each plot would be created as an individual file, unless we add a step to concatenate them.
Probably both from SAMtools stats output
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