Workflow Functionalizing

[cansavvy]

Issue Description

First we need to functionalize all of the steps from https://github.com/FredHutch/GI_mapping/tree/main/workflow/scripts

• pgRNA_counts_QC.Rmd Functionalize Step 1: Quality Control  #3
• filter_and_calculate_LFC.Rmd Functionalize Step 2: Filter and calculate Fold change #4
• get_pgRNA_annotations.Rmd Functionalize Step 3: Annotate #5
• calculate_GI_scores.Rmd Functionalize Step 4: Calculate GI scores #6

Input data

We will be building the pipeline to work on this dataset first:
PP_pgPEN_HeLa_counts.txt

But note that later steps in the pipeline will need a version of this data that is processed up to that point in the pipeline. So we will need to work on these functions sequentially.

General approach

• Take each Rmd linked above, and try to make functions to automate as much of the steps as possible.
• Add software dependency items to the Docker image as they are needed.

Additional goals as we are functionalizing.

• Minimize software dependencies as much as possible
• Look for places where customizations and options may be needed this includes but are not limited to:
  • parameter changes
  • different data structures
  • different annotations needed