Add the check aligner task.

Author: VJalili

src/bash_workflows/check_aligner.sh

@@ -0,0 +1,26 @@
+#!/bin/bash
+
+set -euo pipefail
+
+reads_path=$1
+reads_index=$2
+sample_id=$3
+reference_fasta=${4:-""}
+reference_index=${5:-""}
+reference_dict=${6:-""}
+
+if [[ -n "$reference_fasta" ]]; then
+  ref_opt="-R $reference_fasta"
+else
+  ref_opt=""
+fi
+
+gatk PrintReadsHeader \
+  -I "${reads_path}" \
+  --read-index "${reads_index}" \
+  -O "${sample_id}".header.sam \
+  $ref_opt
+
+awk '$0~"@PG" && $0~"ID: DRAGEN SW build" && $0~"VN: 05.021.604.3.7.8"' "${sample_id}".header.sam \
+  | wc -l \
+  > is_dragen_3_7_8.txt