FastQC, Trimming, Overall QC (initial)

rnaseq/step1_fastqc/snippet.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+#SBATCH --job-name=fastqc
+#SBATCH --time=0-12:00:00
+#SBATCH --ntasks=1
+#SBATCH --mem=15G
+#SBATCH --qos=regular
+
+
+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