callAlign_withDocker.sh

#! /bin/bash

################################################################################
Help()
{
   # Display Help
   echo "This function takes as input two directories: one of cancer predictions and one of lymphocyte predictions. It will align the predictions and generate percent invasion for all included samples, as well as call class as high or low. It will then run survival analyses and generate descriptive statistics."
   echo
   echo "Syntax: callAlign [-a|t|T|c|C|s|o|O|w|h]"
   echo "options:"
   echo "a     (Default: blank) If you know the lymph prediction version you used, listing here will automatically define the Lymph threshold. Acceptable options are r (resnet), v (VGG16), or i (Inception)"
   echo "t     (Default: tilPreds) path to lymph predictions"
   echo "T     (Default: 0.1; Overwritten if -a is provided) Threshold for lymph presence calling at a patch level"
   echo "c     (Default: cancPreds) path to cancer predictions"
   echo "C     (Default: 0.5) Threshold for cancer calling at a patch level "
   echo "s     (OPTIONAL) Only necessary if file names for Lymph and Cancer preds do not exactly match. Path to dataset csv with 3 columns: 1) Sample name, 2) TIL file name, 3) Canc file name"
   echo "o     (Default: Percent_Invasion.csv) Name for csv output"
   echo "O     (Default: outputs) Path to output directory."
   echo "w     Flag to write PNGs of Tumor-TIL maps. Makes dir PNGs/ within output directory"
   echo "S     Flag that the cancer prediction file has patch subtype liklihoods"
   echo "h     Prints this help"
}
################################################################################
## Set Defaults
algorithm='blank'
tilDir='/data/tilPreds'
tilThresh=0.1 
cancDir='/data/cancPreds'
cancThresh=0.5
sampFile='blank'
outputFile='Percent_Invasion.csv'
outputDir='/data/outputs'
writePNG=false
subtypes=false

while getopts :ha:t:T:c:C:s:o:O:wS flag
do
    case "${flag}" in
        h) Help
        exit;;
        a) algorithm=${OPTARG};;
        t) tilDir=${OPTARG};;
        T) tilThresh=${OPTARG};;
        c) cancDir=${OPTARG};;
        C) cancThresh=${OPTARG};;
        s) sampFile=${OPTARG};;
        o) outputFile=${OPTARG};;
        O) outputDir=${OPTARG};;
        w) writePNG=true;;
        S) subtypes=true;;
    esac
done
echo " ======================================================================================== "
echo "Flags specified as the following (BASH parsed): "
echo "algorithm: $algorithm";
echo "tilDir: $tilDir";
echo "tilThresh: $tilThresh";
echo "cancDir: $cancDir";
echo "cancThresh: $cancThresh";
echo "sampFile: $sampFile";
echo "outputFile: $outputFile";
echo "outputDir: $outputDir";
echo "writePNG: $writePNG";
echo "subtypes: $subtypes"
echo " ======================================================================================== "
## Pass these flags to R script for alignment
Rscript commandLineAlign.R $algorithm $tilDir $tilThresh $cancDir $cancThresh $sampFile $outputFile $outputDir $writePNG $subtypes