pgx-main from prod added

pgx-main/upload_results.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+set -xe
+bam_s3_bucket="serenomica-pipeline-archive"
+upload_s3=true
+stellarpgx_ref="stellar_references/cyp2d6_reference_HerCan_v2.bed" #"stellar_references/cyp2d6_reference_pgx_copy.bed" #"stellar_references/cyp2d6_reference_pgx.bed" #"stellar_references/nicole_new_ref.bed"
+
+declare -A vcf_s3_dict
+declare -A bam_s3_dict
+
+FLOWCELL=$1
+RUN=$2
+
+echo "----------------------------------------------------------------"
+
+# --------------------- Upload files to S3 ---------------------------
+if $upload_s3; then
+  for result in $(ls -d pgx_results/*_pgx_result); do
+    sample="${result:12:-11}"
+    vcf_s3_prefix="s3://serenomica-pipeline-data/${FLOWCELL}/${RUN}"
+    bam_s3_prefix="s3://serenomica-pipeline-archive/${RUN}"
+    s3cmd put "${result}/output.json" "${vcf_s3_prefix}/${sample}.json"
+    echo -n "Compressing: "
+    tar -zcvf "${result}.tar.gz" "${result}"
+    s3cmd put "${result}.tar.gz" "${bam_s3_prefix}/"
+  done
+fi
+
+printf "\nDone\n"
+echo "----------------------------------------------------------------"