Create wrappers for STRetch and STRScan

parent 1c9c216b
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_gangstr.sh
## Version : 0.0.1
## Licence : FIXME
## Description : a wrapper for qsubing GangSTR 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_gangstr.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104
## last revision date : 20191104
## Known bugs : None
# Log file path option
if [ -z "$LOGFILE" ]
then
LOGFILE=gangstr.$(date +"%F_%H-%M-%S").log
fi
# Logging
exec 1>> "$LOGFILE" 2>&1
echo "$(date +"%F_%H-%M-%S"): START"
# Check if input file exists
if [ ! -f "$INPUTFILE" ]
then
echo "Input file '$INPUTFILE' does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch gangstr.failed
exit 1
fi
# Check if output prefix is specified
if [ -z "$OUTPUTPREFIX" ]
then
echo "Output prefix is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
touch gangstr.failed
exit 1
fi
# Launch script command and check exit code
echo "command : /work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \
--bam "$INPUTFILE" \
--ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
--regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
--out "$OUTPUTPREFIX" \
--verbose"
/work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \
--bam "$INPUTFILE" \
--ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa \
--regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
--out "$OUTPUTPREFIX" \
--verbose
gangstr_exitcode=$?
echo "gangstr exit code : $gangstr_exitcode"
if [ $gangstr_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
touch gangstr.failed
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_gangstr.sh
## Version : 0.0.1
## Licence : FIXME
## Description : a wrapper for qsubing STRScan script for STR detection
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_strscan.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191115
## last revision date : 20191115
## Known bugs : None
# Log file path option
if [ -z "$LOGFILE" ]
then
LOGFILE=strscan.$(date +"%F_%H-%M-%S").log
fi
# Logging
exec 1>> "$LOGFILE" 2>&1
echo "$(date +"%F_%H-%M-%S"): START"
# Check if input file exists
if [ ! -f "$INPUTFILE" ]
then
echo "Input file '$INPUTFILE' does not exist"
echo "$(date +"%F_%H-%M-%S"): END"
touch strscan.failed
exit 1
fi
# Check if output prefix is specified
if [ -z "$OUTPUTPREFIX" ]
then
echo "Output prefix is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
touch strscan.failed
exit 1
fi
# Launch script command and check exit code
echo "command : /work/gad/shared/bin/strscan/STRScan_2019-11-05/STRScan \
-i "$INPUTFILE" \
-p /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
-o "$OUTPUTFILE""
/work/gad/shared/bin/strscan/STRScan_2019-11-05/STRScan \
-i "$INPUTFILE" \
-p /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed \
-o "$OUTPUTFILE"
strscan_exitcode=$?
echo "strscan exit code : $strscan_exitcode"
if [ $strscan_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
touch gangstr.failed
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"
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