Compare md5sums in a file (output of md5sum) with current md5 of these files

compare_md5.sh

#!/bin/bash

# Read existing md5sums and use to confirm integrity of fastq files

#SBATCH --nodes=1
#SBATCH --cpus-per-task=36
#SBATCH --partition=normal
#SBATCH --time=08:00:00
#SBATCH [email protected]
#SBATCH --job-name=md5checker

module load palma/2021a GCCcore/10.3.0 parallel/20210622

set -ue pipefail

DIR="/path/to/parent/dir/"
JOBS="$SLURM_CPUS_PER_TASK"

# Compare md5sums from a MD5 file with md5sums from files in the same directory.
# Will print to stdout whether ok or not
function CompareMd5Sums {

  MD5FILE="$1"
  BASEDIR="$(dirname $MD5FILE)"
  OUTLOG="${BASEDIR}/$(date +"%Y%m%d"_md5check.txt)"
  awk -F " " -v basedir="$BASEDIR" '{print $1, basedir"/"$2}' < "$MD5FILE" | md5sum -c --status /dev/stdin && echo "$BASEDIR is ok" || echo "$BASEDIR has errors"

}; export -f CompareMd5Sums


find "$DIR" -type f -name 'MD5.txt' | parallel -j "$JOBS" "CompareMd5Sums {}"