Commit 7e8242c8 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Run a rep again.

parent ea5087f8
#!/bin/bash
script_name="run_rep.sh"
#Help function
usage() {
echo "-h --Help documentation for $script_name"
echo "-s --Study_RID."
echo "-r --Rep_RID."
echo "-t --Tag of pipelne"
echo "-e --Email on failure"
echo "-o --Path to output directory"
echo "Example: $script_name -s 16-1ZP0 -r W-RB88 -t 0.1.0 -e 'first.last@utsouthwestern.edu' -o '/path/to/output/dir/'"
exit 1
}
main(){
# Load required modules
module load python/3.6.4-anaconda
module load nextflow/20.01.0
module load singularity/3.5.3
# Parsing options
OPTIND=1 # Reset OPTIND
while getopts :s:r:t:e:o:h opt
do
case $opt in
s) study=$OPTARG;;
r) rid=$OPTARG;;
t) tag=$OPTARG;;
e) email=$OPTARG;;
o) out=$OPTARG;;
h) usage;;
esac
done
shift $(($OPTIND -1))
# Check for mandatory options
if [[ -z $study ]] || [[ -z $rid ]] || [[ -z $tag ]] || [[ -z $email ]] || [[ -z $out ]]; then
usage
fi
# change dir to study
cd $out/$study
cd rna-seq
# run pipeline on replicate RIDs in parallel
echo ${rid}
nextflow -q run workflow/rna-seq.nf --repRID ${rid} --source production --deriva /project/BICF/BICF_Core/shared/gudmap/test_data/auth/credential.json --bdbag /project/BICF/BICF_Core/shared/gudmap/test_data/auth/cookies.txt --dev false --upload true --email ${email} -with-report ./output/${rid}_report.html -with-timeline ./output/${rid}_timeline.html
}
main "$@"
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