md5Checker

Overview

Calculates MD5 checksums for files or verifies files against existing checksums. It supports batch processing via file patterns, file lists, or directory recursion.

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Usage

md5Checker.sh

sbatch --job-name=[jobName] ~/atelier/bin/md5Checker.sh [options] -o [output]

Options

Option	Description
-p [pattern]	File pattern/glob to match files
-f [fileList]	Text file containing list of file paths (one per line)
-s [source]	Source directory to process
-o [output]	In generate mode, checksum file name; In verify mode, existing checksum file to verify against
-v	Verify mode
-r	Recursive mode
-n	Dry run
-a	Append to existing checksum file
-h	Display help message

Examples

Checksum all BAM files in current directory

sbatch --job-name=md5-bams md5Checker.sh \
    -p "*.bam" \
    -o project_bams

Checksum files recursively in a directory

sbatch --job-name=md5-project md5Checker.sh \
    -s /data/project/ \
    -r -o project_backup

Checksum files from a list

sbatch --job-name=md5-list md5Checker.sh \
    -f files_to_check.txt \
    -o my_files

Checksum specific pattern recursively

sbatch --job-name=md5-fastq md5Checker.sh \
    -s /data/fastq/ \
    -p "*.fastq.gz" \
    -r -o fastq_files

Dry run to preview

sbatch --job-name=md5-preview md5Checker.sh \
    -p "*.bam" \
    -o test -n

Append to existing checksum file

sbatch --job-name=md5-append md5Checker.sh \
    -p "*.cram" \
    -o project_bams -a

Verify all files in a checksum file

sbatch --job-name=md5-verify md5Checker.sh \
    -v \
    -o md5sums-project_bams.txt

Verify only specific files against checksum file

sbatch --job-name=md5-verify-bams md5Checker.sh \
    -v \
    -p "*.bam" \
    -o md5sums-project_bams.txt

Verify files from a list

sbatch --job-name=md5-verify-list md5Checker.sh \
    -v \
    -f files_to_verify.txt\
    -o md5sums-project.txt

Dry run verification

sbatch --job-name=md5-verify-preview md5Checker.sh \
    -v \
    -o md5sums-project.txt -n

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