incomplete download of pgx-main

pgx-main/download_files.sh

@@ -1,28 +0,0 @@
-#!/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