forked from GRIAC/system_genetics
fastqc: simple comment. trimming: reverted back. overall qc: simplified the scripts and made sure to add instructions.
This commit is contained in:
@ -1,34 +1,5 @@
|
||||
#!/bin/bash
|
||||
#SBATCH --job-name=fastqc
|
||||
#SBATCH --time=0-12:00:00
|
||||
#SBATCH --ntasks=1
|
||||
#SBATCH --mem=15G
|
||||
#SBATCH --qos=regular
|
||||
# The command to do a FastQC on a fastq file is
|
||||
file="file_to_analyse.fq.gz"
|
||||
fastqc_out="./path/to/fastqc/output/dir"
|
||||
|
||||
|
||||
set -e
|
||||
set -u
|
||||
set -x
|
||||
set -o pipefail
|
||||
|
||||
|
||||
module purge
|
||||
module load Java
|
||||
module load FastQC
|
||||
|
||||
|
||||
dir_raw_fastq="$(pwd)/fastq/raw"
|
||||
dir_fastqc="$(pwd)/fastqc"
|
||||
|
||||
|
||||
[ -d "${dir_fastqc}" ] || mkdir -p "${dir_fastqc}"
|
||||
|
||||
|
||||
# Run FastQC
|
||||
files=$(find -L "$dir_raw_fastq" -type f -iname "*.fastq.gz")
|
||||
for file in $files; do
|
||||
filename=$(basename "$file")
|
||||
fastqc -o "$dir_fastqc" "$file" &
|
||||
done
|
||||
|
||||
wait
|
||||
fastqc -o "$fastqc_out" "$file"
|
||||
|
Reference in New Issue
Block a user