Rename wrapper_ehdn.sh to wrapper_ehdn_profile.sh

parent 16f9d1ec
......@@ -14,7 +14,7 @@
- `wrapper_delete.sh`
- `wrapper_ehdn.sh`
- `wrapper_expansionhunter.sh`
- `wrapper_gangstre.sh`
- `wrapper_gangstr.sh`
- `wrapper_transfer.sh`
- `wrapper_tredparse.sh`
4. Launch `getResults.py`. Warning, don't overwrite existing files.
......
......@@ -17,8 +17,8 @@ LOGFILE="$OUTPUTDIR/$DATE.log"
if [ $# -eq 1 ] && [ "x$1" = x--local ]
then
mkdir -p "$OUTPUTDIR"
INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn.sh"
INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn_profile.sh"
else
mkdir -p "$OUTPUTDIR"
qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_ehdn.sh
qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_ehdn_profile.sh
fi
......@@ -55,7 +55,7 @@ qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "gangstr_$SAMPLE" -hold_jid "$TRANSFER_JOB"
# Launch ehdn profile
mkdir -p "$OUTPUTDIR/ehdn"
qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "ehdn_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn.sh
qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "ehdn_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn_profile.sh
# Delete transfered bam and bai
if [ "x$TRANSFER" = "xyes" ]
......
......@@ -5,7 +5,7 @@
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: a wrapper for qsubing ExpansionHunter denovo script for STR detection
## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_ehdn.sh
## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_ehdn_profile.sh
# Source the configuration file
. "$(dirname "$0")/config.sh"
......
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