Retired-DOME2/DOME2s03_multiQC.sh at main · dantaslab/Retired-DOME2 · GitHub

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#!/bin/bash
#===============================================================================
# Name         : s03_multiQC.sh
# Description  : This script will run multiqc on a large number of files
# Usage        : sbatch s03_multiQC.sh
# Author       : Ai Zhang, ai.z@wustl.edu
# Version      : 1.0
# Created On   : 2023_08_23
#===============================================================================
#
#Submission script for HTCF
#SBATCH --job-name=multiqc
#SBATCH --mem=20G
#SBATCH --output=slurm/multiQC/z_multiqc_%A_%a.out
#SBATCH --error=slurm/multiQC/z_multiqc_%A_%a.out
#SBATCH --mail-user=paruthiyil@wustl.edu
#SBATCH --mail-type=END
#SBATCH --mail-type=FAIL

eval $( spack load --sh py-multiqc)

basedir="/scratch/gdlab/p.sri/240601_DOME2/RNA/250626_data"
rawin="/scratch/gdlab/p.sri/240601_DOME2/RNA/250626_data/concatreads"
indir="${basedir}/d02_read_qc"
#rawin="/lts/gdlab/raw_data/2025/250505_DOME2_CM_SP_SR_RESEQ3"
cleanin="/scratch/gdlab/p.sri/240601_DOME2/RNA/250626_data/d01a_trimmomatic"
rawout="${indir}/raw_reads/multiqc"
cleanout="${indir}/clean_reads/multiqc"

#mkdir -p ${outdir}

set -x
time sh -c \
"multiqc ${rawin} -o ${rawout} -n raw_multiqc; \
multiqc ${cleanin} -o ${cleanout} -n clean_multiqc"
RC=$?
set +x

if [ $RC -eq 0 ]
then
  echo "Job completed successfully"
else
  echo "Error Occured in ${sample}!"
  exit $RC
fi