A script to summarize FASTQC results to be included in an email.

fastqc_to_email.sh

#!/bin/bash

# Usage:
#  $ bash fastqc_to_email.sh REPORT_HEADER /path/to/file1.html /path/to/file2.html ...
#
# requires the unzipped folder containing the summaries to be present in the same folder
# with the HTML report!

JOB_NAME=$1
echo "# FASTQC ran for $JOB_NAME"
shift

# Convert html paths into their summary counter-parts
SUMMARY_FILES=$(echo "$@" |sed -e 's/\.html/\/summary.txt/g')

for qcsummary in $SUMMARY_FILES
do
  NUM_OF_PASSES=$(cat ${qcsummary} |grep PASS |wc -l |awk '{ print $1 }')
  NUM_OF_CHECKS=$(cat ${qcsummary} |wc -l |awk '{ print $1 }')

  echo "## File: $qcsummary"
  echo "## Result: $NUM_OF_PASSES/$NUM_OF_CHECKS passed"
  echo "## Issues: "
  cat ${qcsummary} |grep -v "PASS" |cut -f1,2 |sed -e 's/^/ - /g'
  echo -en "\n"
done