Examine Fastqc reports in aggregate; brings images, statistics, and summaries together. #fastq

FastQC_aggregate.sh

#!/bin/bash
# Run this script in project root--expected structure: `./fastqc/<sample>/*.zip`
# This script aggregates images of each type in individual folders
# o looking across data is quick.

zips=`ls fastqc/*/*.zip`

for i in $zips; do
    unzip -oq -d "$(dirname "$i")" $i;
done

fastq_folders=${zips/.zip/}

aggregate_folder=fastqc/aggregated
rm -rf "$aggregate_folder" # Remove aggregate folder if present
mkdir "$aggregate_folder"

# Rename Files within each using folder name.
for folder in $fastq_folders; do
    folder=${folder%.*}
    img_files=`ls ${folder}/Images/*png`;
    for img in $img_files; do
        img_name=$(basename "$img");
        img_name=${img_name%.*}
        new_name=${folder};
        new_name="$(basename "${folder/_fastqc/}")"
        mkdir -p "${aggregate_folder}"/${img_name};
        mv $img "${aggregate_folder}"/${img_name}/${new_name}.png;
    done;
done;


# Concatenate Summaries
for folder in $fastq_folders; do
    folder=${folder%.*}
    cat ${folder}/summary.txt >> "${aggregate_folder}"/summary.txt
done;

# Concatenate Statistics
for folder in $fastq_folders; do
    folder=${folder%.*}
    head -n 10 ${folder}/fastqc_data.txt | tail -n 7 | awk -v f=${folder/_fastqc/} '{ print $0 "\t" f }' >> "${aggregate_folder}"/statistics.txt
    rm -rf ${folder}
done

Modified for different directory structure and DRY aggregate folder