Handle optional transfer from an archive directory

README.md

@@ -24,3 +24,6 @@
 8. Change z-score threshold if necessary in `triplets_outliers.py`.
 9. Launch `launch_triplets_outliers.sh`. Dependency: `patho.csv`.
 10. Get files (i.e.: `scp 'an1770de@ssh-ccub.u-bourgogne.fr:/work/gad/shared/analyse/STR/results/*' .`)
+
+
+Dans doc : préciser que le répertoire input doit être différent du répertoire d'output (précaution pour éviter de supprimer données brutes)
\ No newline at end of file

pipeline.sh

@@ -21,31 +21,46 @@ 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
+
 INPUTFILE="INPUTDIR/$SAMPLE.bam"
 DATE="$(date +"%F_%H-%M-%S")"
 OUTPUTDIR="OUTPUTDIR/$SAMPLE"
+TRANSFER_JOB=""
 
 # Transfer bam and bai from archive to work
-mkdir -p "$OUTPUTDIR"
-qsub -pe smp 1 -q "$TRANSFERQUEUE" -N "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" wrapper_transfer.sh
-
-INPUTFILE="$OUTPUTDIR/$SAMPLE.bam"
+if [ "x$TRANSFER" = "xyes" ]
+then
+    mkdir -p "$OUTPUTDIR"
+    TRANSFER_JOB="transfer_$SAMPLE"
+    qsub -pe smp 1 -q "$TRANSFERQUEUE" -N "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" wrapper_transfer.sh
+    INPUTFILE="$OUTPUTDIR/$SAMPLE.bam"
+fi
 
 # Launch ExpansionHunter
 mkdir -p "$OUTPUTDIR/eh"
-qsub -pe smp 4 -q "$COMPUTEQUEUE"  -N "eh_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/eh/$SAMPLE",LOGFILE="$OUTPUTDIR/eh/$DATE.log" wrapper_expansionhunter.sh
+qsub -pe smp 4 -q "$COMPUTEQUEUE"  -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 "$OUTPUTDIR/tredparse"
-qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "tredparse_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR/tredparse",LOGFILE="$OUTPUTDIR/tredparse/$DATE.log" wrapper_tredparse.sh
+qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "tredparse_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR/tredparse",LOGFILE="$OUTPUTDIR/tredparse/$DATE.log" wrapper_tredparse.sh
 
 # Launch GangSTR
 mkdir -p "$OUTPUTDIR/gangstr"
-qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "gangstr_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/gangstr/$SAMPLE",LOGFILE="$OUTPUTDIR/gangstr/$DATE.log" wrapper_gangstr.sh
+qsub -pe smp 4 -q "$COMPUTEQUEUE" -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 "$OUTPUTDIR/ehdn"
-qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "ehdn_$SAMPLE" -hold_jid "transfer_$SAMPLE" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn.sh
+qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "ehdn_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn.sh
 
 # Delete transfered bam and bai
-qsub -pe smp 1 -q "$COMPUTEQUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -v SAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log" wrapper_delete.sh
+if [ "x$TRANSFER" = "xyes" ]
+then
+    qsub -pe smp 1 -q "$COMPUTEQUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -v SAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log" wrapper_delete.sh
+else
+    qsub -pe smp 1 -q "$COMPUTEQUEUE" -N "delete_$SAMPLE" -hold_jid "eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE" -sync y -b y echo "Nothing to delete."
+fi