Create log files in the output directory

parent 365a361c
......@@ -38,30 +38,30 @@ if [ "x$TRANSFER" = "xyes" ]
then
mkdir -p "$OUTPUTDIR"
TRANSFER_JOB="transfer_$SAMPLE"
qsub -wd "$WD" -pe smp 1 -q "$TRANSFER_QUEUE" -N "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",TRANSFER_OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" wrapper_transfer.sh
qsub -wd "$WD" -pe smp 1 -o "$OUTPUTDIR" -e "$OUTPUTDIR" -q "$TRANSFER_QUEUE" -N "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",TRANSFER_OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" wrapper_transfer.sh
INPUTFILE="$OUTPUTDIR/$SAMPLE.bam"
fi
# Launch ExpansionHunter
mkdir -p "$OUTPUTDIR/eh"
qsub -wd "$WD" -pe smp 4 -q "$COMPUTE_QUEUE" -N "eh_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/eh/$SAMPLE",LOGFILE="$OUTPUTDIR/eh/$DATE.log" wrapper_expansionhunter.sh
qsub -wd "$WD" -pe smp 4 -o "$OUTPUTDIR" -e "$OUTPUTDIR" -q "$COMPUTE_QUEUE" -N "eh_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/eh/$SAMPLE",LOGFILE="$OUTPUTDIR/eh/$DATE.log" wrapper_expansionhunter.sh
# Launch Tredparse
mkdir -p "$OUTPUTDIR/tredparse"
qsub -wd "$WD" -pe smp 4 -q "$COMPUTE_QUEUE" -N "tredparse_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",TREDPARSE_OUTPUTDIR="$OUTPUTDIR/tredparse",LOGFILE="$OUTPUTDIR/tredparse/$DATE.log" wrapper_tredparse.sh
qsub -wd "$WD" -pe smp 4 -o "$OUTPUTDIR" -e "$OUTPUTDIR" -q "$COMPUTE_QUEUE" -N "tredparse_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",TREDPARSE_OUTPUTDIR="$OUTPUTDIR/tredparse",LOGFILE="$OUTPUTDIR/tredparse/$DATE.log" wrapper_tredparse.sh
# Launch GangSTR
mkdir -p "$OUTPUTDIR/gangstr"
qsub -wd "$WD" -pe smp 4 -q "$COMPUTE_QUEUE" -N "gangstr_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/gangstr/$SAMPLE",LOGFILE="$OUTPUTDIR/gangstr/$DATE.log" wrapper_gangstr.sh
qsub -wd "$WD" -pe smp 4 -o "$OUTPUTDIR" -e "$OUTPUTDIR" -q "$COMPUTE_QUEUE" -N "gangstr_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/gangstr/$SAMPLE",LOGFILE="$OUTPUTDIR/gangstr/$DATE.log" wrapper_gangstr.sh
# Launch ehdn profile
mkdir -p "$OUTPUTDIR/ehdn"
qsub -wd "$WD" -pe smp 4 -q "$COMPUTE_QUEUE" -N "ehdn_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn_profile.sh
qsub -wd "$WD" -pe smp 4 -o "$OUTPUTDIR" -e "$OUTPUTDIR" -q "$COMPUTE_QUEUE" -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" ]
then
qsub -wd "$WD" -pe smp 1 -q "$COMPUTE_QUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -v SAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log" wrapper_delete.sh
qsub -wd "$WD" -pe smp 1 -o "$OUTPUTDIR" -e "$OUTPUTDIR" -q "$COMPUTE_QUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -v SAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log" wrapper_delete.sh
else
qsub -wd "$WD" -pe smp 1 -q "$COMPUTE_QUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -b y echo "Nothing to delete."
qsub -wd "$WD" -pe smp 1 -o "$OUTPUTDIR" -e "$OUTPUTDIR" -q "$COMPUTE_QUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -b y echo "Nothing to delete."
fi
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