- [ ] Ajouter le sample dans le nom de fichier de log
- [ ] Ajouter le sample dans le nom de fichier de log pour pieline.sh
- [ ] Changer le répertoire de sortie : /STR/pipeline car pipeline n'est pas explicite (répertoire avec fichiers de sortie des outils de détection de STR)
qsub -pe smp 1 -q"$COMPUTE_QUEUE"-N"delete_$SAMPLE"-hold_jid"eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE"-sync y -vSAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log""$(dirname"$0")/wrapper_delete.sh"
qsub -wd"$WD"-pe smp 1 -q"$COMPUTE_QUEUE"-N"delete_$SAMPLE"-hold_jid"eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE"-sync y -vSAMPLE="$SAMPLE",LOGFILE="$OUTPUTDIR/delete_$DATE.log" wrapper_delete.sh
else
qsub -pe smp 1 -q"$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 -q"$COMPUTE_QUEUE"-N"delete_$SAMPLE"-hold_jid"eh_$SAMPLE,tredparse_$SAMPLE,gangstr_$SAMPLE,ehdn_$SAMPLE"-sync y -b y echo"Nothing to delete."
## Description: a wrapper for qsubing bam transfer for STR pipeline
## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_transfer.sh
## 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
## Description: a wrapper for qsubing Tredparse script for STR detection
## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_tredparse.sh
## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,TREDPARSE_OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_tredparse.sh