Convert QC/QA notebooks to scripts

[sapoudel]

We should try to minimize notebook usage as much as possible. They can lead to issues if the cells are not run the in the exact order and they require more manual work when compared to scripts. We can convert the QC/QA notebooks to scripts that outputs everything the user needs to know to run QC/QA (e.g. cluster figure, pearson correlation between replicates etc.) and the user can change the input parameters to the script to change QC thresholds.