FastQC - NBISweden/workshop-genome_assembly GitHub Wiki

Notes:

• Gzip flags an error when the file is incomplete (i.e. EOF not found)

Command:

#!/usr/bin/env bash

module load bioinfo-tools FastQC

CPUS="${SLURM_NPROCS:-6}"
JOB=$SLURM_ARRAY_TASK_ID

DATA_DIR=/path/to/reads
FILES=( $DATA_DIR/*_R1.fastq.gz )

FASTQ=${FILES[$JOB]}
fastqc -t "$CPUS" "$FASTQ" "${FASTQ/_R1./_R2.}"