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