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#! /bin/sh
### ASDP PIPELINE ###
## Version: 0.0.1
## Licence: AGPLv3
## Author: Anne-Sophie Denommé-Pichon
## Description: a wrapper for qsubing ExpansionHunter 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_expansionhunter.sh
# Source the configuration file
. ./config.sh
# Log file path option
if [ -z "$LOGFILE" ]
then
LOGFILE=expansionhunter.$(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 "$(date +"%F_%H-%M-%S"): END"
exit 1
fi
# Check if output prefix is specified
if [ -z "$OUTPUTPREFIX" ]
then
echo "Output prefix is not specified"
echo "$(date +"%F_%H-%M-%S"): END"
exit 1
fi
# Create .bam and .bai symbolic links (EH expects .bam.bai)
TMPDIR="$(mktemp -d)"
ln -s "$INPUTFILE" "$TMPDIR/$(basename "$INPUTFILE")"
if [ -f "$INPUTFILE.bai" ]
then
ln -s "$INPUTFILE.bai" "$TMPDIR/$(basename "$INPUTFILE").bai"
else
ln -s "$(echo "$INPUTFILE" | sed 's/\.bam$/.bai/')" "$TMPDIR/$(basename "$INPUTFILE").bai"
fi
# Launch script command and check exit code
echo "command : $EH \
--reads $TMPDIR/$(basename "$INPUTFILE") \
--reference $REF \
--variant-catalog $EH_VARIANT_CATALOG \
--output-prefix $OUTPUTPREFIX"
"$EH" \
--reads "$TMPDIR/$(basename "$INPUTFILE")" \
--reference "$REF" \
--variant-catalog "$EH_VARIANT_CATALOG" \
--output-prefix "$OUTPUTPREFIX"
expansionhunter_exitcode=$?
# Remove .bam and .bai symbolic links
rm "$TMPDIR/$(basename "$INPUTFILE")"
rm "$TMPDIR/$(basename "$INPUTFILE").bai"
rmdir "$TMPDIR"
echo "expansionhunter exit code : $expansionhunter_exitcode"
if [ $expansionhunter_exitcode != 0 ]
then
echo "$(date +"%F_%H-%M-%S"): END"
exit 1
fi
echo "$(date +"%F_%H-%M-%S"): END"