incomplete download of pgx-main

pgx-main/upload_results.sh

@@ -1,29 +0,0 @@
-#!/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 "----------------------------------------------------------------"