#!/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 "----------------------------------------------------------------"