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fastqc.sh
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fastqc.sh
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#!/bin/bash
#SBATCH -p # put comma separated list of available partitions here
#SBATCH -n 1 # Number of cores
#SBATCH -t 0-3:00 # Runtime in days-hours:minutes
#SBATCH --mem 6000 # Memory in MB
#SBATCH -J FastQC # job name
#SBATCH -o FastQC.%A.out # File to which standard out will be written
#SBATCH -e FastQC.%A.err # File to which standard err will be written
##SBATCH --mail-type=ALL # Type of email notification- BEGIN,END,FAIL,ALL
##SBATCH --mail-user=<PUT YOUR EMAIL ADDRESS HERE> # Email to which notifications will be sent
"""
For this script to initialize a conda environment, a version of python that supports
anaconda or mamba will need to be in PATH. In a case where the HPC environment has python
available as a loadable module, such as the Harvard Cannon cluster,
it will simply require adding: module load python.
"""
source activate fastqc
infile=$1 # $1 represent the first (and in this case only) command line argument supplied to the script
echo "infile is $infile"
fastqc --outdir `pwd`/fastqc $infile