29 lines
706 B
Bash
29 lines
706 B
Bash
#!/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
|