FastQC, Trimming, Overall QC (initial)

rnaseq/step2_trim/snippet.sh

@@ -0,0 +1,64 @@
+#!/bin/bash
+#SBATCH --job-name=trimming
+#SBATCH --time=2-00:00:00
+#SBATCH --ntasks=1
+#SBATCH --mem=15G
+#SBATCH --qos=regular
+
+
+set -e
+set -u
+set -x
+set -o pipefail
+
+
+module purge
+module load TrimGalore
+
+
+dir_raw_fastq="$(pwd)/fastq/raw"
+dir_trimmed_fastq="$(pwd)/fastq/trimmed"
+dir_trimmed_fastq_reports="$(pwd)/fastq/trimmed/reports"
+
+adapter_3p="TGGAATTCTCGG" # is _R1
+adapter_5p="GATCGTCGGACT" # is _R2
+
+
+[ -d "${dir_trimmed_fastq_reports}" ] || mkdir -p "${dir_trimmed_fastq_reports}"
+
+
+# Trim all adapters from the sequences
+while IFS=, read -r GSID Sample
+do
+  echo ">> Executing trimming of $GSID (${#GSID})"
+  if [ "${#GSID}" == "18" ]; then # check length - don't include sample pools
+    for fqFile in $(find -L "$dir_raw_fastq" -maxdepth 1 -type f -iname "*${GSID}*.fastq.gz"); do
+      newFilename=${fqFile/.fastq.gz/_trimmed.fq.gz}
+      if [ -f "${newFilename}" ]; then
+        echo ">>File exists ${newFilename}. Skipping"
+      else
+        echo ">>File: ${fqFile}"
+        if grep -q "_R1" <<< $(basename "$fqFile"); then
+          adapter_seq=$adapter_3p
+        elif grep -q "_R2" <<< $(basename "$fqFile"); then
+          adapter_seq=$adapter_5p
+        fi
+        echo ">>Trimming with sequence ${adapter_seq}"
+        trim_galore \
+          --adapter "$adapter_seq" \
+          --length $(printf "$adapter_seq" | wc -m) \
+          --output_dir "${dir_trimmed_fastq}" \
+          --fastqc_args "--noextract" \
+          "${fqFile}" &
+      fi
+    done
+  else
+    echo "Skipped."
+  fi
+done < samples.csv
+
+
+wait
+mv ${dir_trimmed_fastq}/*.zip "${dir_trimmed_fastq_reports}"
+mv ${dir_trimmed_fastq}/*.txt "${dir_trimmed_fastq_reports}"
+mv ${dir_trimmed_fastq}/*.html "${dir_trimmed_fastq_reports}"