Support Modules: panoply_cna_setup

panoply_cna_setup

Description

This module sets up directories and code for running CNA analysis.

Input

Required inputs:

• tarball: (.tar file) tarball from panoply_harmonize
• type: (String) data type
• yaml: (.yaml file) master-parameters.yaml

Optional inputs:

• groupsFile: (.csv file) subset of sample annotations
• peMaxDefault: (Int, default = 250) default maximum processors/jobs for parallelism
• minCnaN: (Int, default = 5) minimum number of samples required to perform CNA correlation analysis
• outFile: (String, default = "panoply_cna_setup-output.tar") output .tar file name

Output

• outputs: Tarball including the following files in the cna subdirectory:
  • Harmonized data matrices for CNA (all-cna-matrix.csv), RNA (all-rna-matrix.csv) and proteome (all-pome-matrix.csv)
  • A text file file_table.tsv listing all the data matrix files