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#! /bin/sh
### ASDP PIPELINE ###
## Version: 0.0.1
## Licence: AGPLV3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: a wrapper for qsubing bam deletion for STR pipeline
## Usage: qsub -pe smp 1 -v SAMPLE=<sample>,[LOGFILE=<path to the log file>] wrapper_delete.sh
# Source the configuration file
. ./config.sh
# Log file path option
if [ -z "$LOGFILE" ]
then
LOGFILE=delete.$(date +"%F_%H-%M-%S").log
fi
# Logging
exec 1>> "$LOGFILE" 2>&1
echo "$(date +"%F_%H-%M-%S"): START"
# Check if sample is specified
if [ -z "$SAMPLE" ]
then
echo "Sample is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
exit 1
fi
# Delete and check exit code
echo "command : rm \
$SAMPLE"
rm \
"$OUTPUTDIR/$SAMPLE/$SAMPLE.bam" \
"$OUTPUTDIR/$SAMPLE/$SAMPLE.bai"
delete_exitcode=$?
echo "delete exit code : $delete_exitcode"
if [ $delete_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"