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Multi_FASTQC.sh
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#!/bin/bash
#SBATCH --job-name=Multi_fastqc
#SBATCH -o /hb/home/miclark/kelpEVOL_fq_gz_processing/logs/Multi_fastqc-%j.out
#SBATCH --cpus-per-task=6 # originally 32, changing to 2 for testing
#SBATCH --time=01:00:00
#SBATCH --mem=20G # originally 100, changing to 10 for testing
#SBATCH --partition=lab-mpinsky
#SBATCH --qos=pi-mpinsky
#SBATCH --account=pi-mpinsky
############# Multi_FASTQC.sh ###################
## runs FASTQC and MultiQC reports in parallel ##
## contact: Eric Garcia, [email protected] ##
## mic updated this 2025-02-05 for UCSC hb ##
#################################################
## Requirements: parallel, fastqc, and multiqc in current session
## To execute, type in the command line (do include quotes):
# sbatch Multi_FASTQC.sh "<extension of files to be processed in quotations>" "<full path to directory with the files to be processed>"
#### Details
# Multi_FASTQC.sh is a simple sbatch script that runs FASTQC and MultiQC reports in parallel with a single command
# Results will be directed to a newly created sub-directory called Multi_FASTQC
# For FASQC options use <fasqc --help> or visit https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
# For MultiQC options use <multiqc --help> or visit https://multiqc.info/
## Script Usage:
# 1.- Set the above slurm settings (#SBATCH) according to your system. Change the filepath where the outfile is generated.
# 2.- Load parallel, fastqc and multiqc according to your system. Example:
#
module load parallel/20200122
# module load multiqc/1.27
module load fastqc/0.12.1
module list
# 3.- Execute the script
# in the command line, type "sbatch", the name of the script <Multi_FASTQC.sh>, the FULL path to the files to be processed, the desired name for the multiQC report and the suffix identifying the files to be analyzed in quotations. The last can be file extensions or any other shared file identifier at the end of the files' names, and the full path to the directory containing the files to be processed
# example: <sbatch Multi_FASTQC.sh "indir" "mqc report name" "file extension to qc">
# Alternately, the suffix can be replaced by any regex expression that correctly identifies the files to be processed.
# If such regex does not occur at the end of file names, you'll need to remove the wild card " * " in the first fastqc statement in line 55
# Multi_FASTQC.sh has been tested in "fq", "fq.gz" and "bam" files.
#inDIR=$(echo $1 | sed 's/\\/$//')
inDIR=$1
REPORTNAME=$2
PATTERN=$3
#run fastqc in parallel
ls ${inDIR}/*${PATTERN} | parallel --no-notice -j2 "fastqc {}" # change number after "j" to the number of cpus requested
# load multiqc
module unload fastqc/0.12.1
module load multiqc/1.27
# run multiqc with specific report and subdirectory names
# removed crun functionality for hummingbird
multiqc -v -p -ip -f --data-dir --data-format tsv --cl-config "max_table_rows: 3000" --filename $REPORTNAME --outdir $inDIR $inDIR
# move fastqc files to new subdirectory
#ls *fastqc.html | parallel -kj 32 "mv {} ../Multi_FASTQC" &&
#ls *fastqc.zip | parallel -kj 32 "mv {} ../Multi_FASTQC"
#mv *out ${inDIR}/logs # change to match log dir where you want your log files to live