pgx-main from prod added

pgx-main/download_files.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+
+bam_s3_bucket="quantgene-wes-archive"
+upload_s3=true
+
+file=${1--}
+
+# --------------------- Download files from S3 -----------------------
+while IFS= read vcf_s3; do
+  temp=($(echo $vcf_s3 | tr "/" "\n"))
+  vcf_s3_bucket="${temp[1]}"
+  flowcell="${temp[2]}"
+  run="${temp[3]}"
+  sample="${temp[4]::-4}"
+  
+  vcf_s3_prefix="s3://${vcf_s3_bucket}/${flowcell}/${run}"
+  bam_s3_prefix="s3://${bam_s3_bucket}/${run}"
+  
+  bam_s3="${bam_s3_prefix}/${sample}.deduped.bam"
+  aws s3 cp $vcf_s3 data/
+  aws s3 cp $bam_s3 data/
+done < <(cat -- "$file")
+
+# ------------------------ Index BAM files ---------------------------
+for f in data/*.bam; do
+  echo "Indexing: "$f
+  samtools index $f $f".bai"
+done