Place output files in specific directories

parent 77c7b4f9
......@@ -21,11 +21,12 @@ fi
# Source the configuration file
. "$(dirname "$0")/config.sh"
if [ "x$INPUTDIR" = "x$OUTPUTDIR" ]
then
echo "Input directory is the same as output directory. Please change it to prevent the pipeline from deleting or overwriting raw data."
exit 1
fi
# Commented to fit the GAD pipeline
#if [ "x$INPUTDIR" = "x$OUTPUTDIR" ]
#then
# echo "Input directory is the same as output directory. Please change it to prevent the pipeline from deleting or overwriting raw data."
# exit 1
#fi
INPUTFILE="$INPUTDIR/$SAMPLE.bam"
DATE="$(date +"%F_%H-%M-%S")"
......@@ -33,35 +34,39 @@ OUTPUTDIR="$OUTPUTDIR/$SAMPLE"
TRANSFER_JOB=""
WD="$(dirname "$(readlink -f "$0")")"
LOGDIR="$OUTPUTDIR/logs"
STRDIR="$OUTPUTDIR/str"
mkdir -p "$LOGDIR" "$STRDIR"
# Transfer bam and bai from archive to work
if [ "x$TRANSFER" = "xyes" ]
then
mkdir -p "$OUTPUTDIR"
TRANSFER_JOB="transfer_$SAMPLE"
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_$DATE.log" "$WD/wrapper_transfer.sh"
INPUTFILE="$OUTPUTDIR/$SAMPLE.bam"
qsub -wd "$WD" -pe smp 1 -o "$LOGDIR" -e "$LOGDIR" -q "$TRANSFER_QUEUE" -N "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",TRANSFER_OUTPUTDIR="$STRDIR",LOGFILE="$LOGDIR/transfer_$SAMPLE.$DATE.log" "$WD/wrapper_transfer.sh"
INPUTFILE="$STRDIR/$SAMPLE.bam"
fi
# Launch ExpansionHunter
mkdir -p "$OUTPUTDIR/eh"
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/$DATE.log" "$WD/wrapper_expansionhunter.sh"
mkdir -p "$STRDIR/eh"
qsub -wd "$WD" -pe smp 4 -o "$LOGDIR" -e "$LOGDIR" -q "$COMPUTE_QUEUE" -N "eh_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$STRDIR/eh/$SAMPLE",LOGFILE="$LOGDIR/eh_$SAMPLE.$DATE.log" "$WD/wrapper_expansionhunter.sh"
# Launch Tredparse
mkdir -p "$OUTPUTDIR/tredparse"
qsub -wd "$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/$DATE.log" "$WD/wrapper_tredparse.sh"
mkdir -p "$STRDIR/tredparse"
qsub -wd "$WD" -pe smp 4 -o "$LOGDIR" -e "$LOGDIR" -q "$COMPUTE_QUEUE" -N "tredparse_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",TREDPARSE_OUTPUTDIR="$STRDIR/tredparse",LOGFILE="$LOGDIR/tredparse_$SAMPLE.$DATE.log" "$WD/wrapper_tredparse.sh"
# Launch GangSTR
mkdir -p "$OUTPUTDIR/gangstr"
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/$DATE.log" "$WD/wrapper_gangstr.sh"
mkdir -p "$STRDIR/gangstr"
qsub -wd "$WD" -pe smp 4 -o "$LOGDIR" -e "$LOGDIR" -q "$COMPUTE_QUEUE" -N "gangstr_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$STRDIR/gangstr/$SAMPLE",LOGFILE="$LOGDIR/gangstr_$SAMPLE.$DATE.log" "$WD/wrapper_gangstr.sh"
# Launch ehdn profile
mkdir -p "$OUTPUTDIR/ehdn"
qsub -wd "$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" "$WD/wrapper_ehdn_profile.sh"
mkdir -p "$STRDIR/ehdn"
qsub -wd "$WD" -pe smp 4 -o "$LOGDIR" -e "$LOGDIR" -q "$COMPUTE_QUEUE" -N "ehdn_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$STRDIR/ehdn/$SAMPLE",LOGFILE="$LOGDIR/ehdn_$SAMPLE.$DATE.log" "$WD/wrapper_ehdn_profile.sh"
# Delete transfered bam and bai
if [ "x$TRANSFER" = "xyes" ]
then
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" "$WD/wrapper_delete.sh"
else
qsub -wd "$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
#if [ "x$TRANSFER" = "xyes" ]
#then
# qsub -wd "$WD" -pe smp 1 -o "$LOGDIR" -e "$LOGDIR" -q "$COMPUTE_QUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -v SAMPLE="$SAMPLE",LOGFILE="$LOGDIR/delete_$SAMPLE.$DATE.log" "$WD/wrapper_delete.sh"
#else
qsub -wd "$WD" -pe smp 1 -o "$LOGDIR" -e "$LOGDIR" -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
......@@ -32,8 +32,8 @@ fi
echo "command : rm \
$SAMPLE"
rm \
"$OUTPUTDIR/$SAMPLE/$SAMPLE.bam" \
"$OUTPUTDIR/$SAMPLE/$SAMPLE.bai"
"$OUTPUTDIR/$SAMPLE/str/$SAMPLE.bam" \
"$OUTPUTDIR/$SAMPLE/str/$SAMPLE.bai"
delete_exitcode=$?
......
......@@ -7,7 +7,6 @@
## Description: a wrapper for qsubing bam transfer for STR pipeline
## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,TRANSFER_OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_transfer.sh
# Log file path option
if [ -z "$LOGFILE" ]
then
......
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