Fix some bugs

TODO.org

@@ -9,6 +9,6 @@
   - [ ] Brancher EHDN et outlier
   - [ ] Séparer case et contrôles
   - [ ] Ajouter EHDN dans GetResults
-- [ ] 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)
 - [ ] Remove dijen from str_outliers.py

pipeline.sh

@@ -21,46 +21,47 @@ fi
 # Source the configuration file
 . "$(dirname "$0")/config.sh"
 
-if [ "x$INPUTDIR" = "x$OUTPUTDIR"]
+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/$SAMPLE.bam"
+INPUTFILE="$INPUTDIR/$SAMPLE.bam"
 DATE="$(date +"%F_%H-%M-%S")"
-OUTPUTDIR="OUTPUTDIR/$SAMPLE"
+OUTPUTDIR="$OUTPUTDIR/$SAMPLE"
 TRANSFER_JOB=""
+WD="$(dirname "$(readlink -f "$0")")"
 
-# Transfer bam and bai from archive to work
+Transfer bam and bai from archive to work
 if [ "x$TRANSFER" = "xyes" ]
 then
     mkdir -p "$OUTPUTDIR"
     TRANSFER_JOB="transfer_$SAMPLE"
-    qsub -pe smp 1 -q "$TRANSFER_QUEUE" -N "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" "$(dirname "$0")/wrapper_transfer.sh"
+    qsub -wd "$WD" -pe smp 1 -q "$TRANSFER_QUEUE" -N "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",TRANSFER_OUTPUTDIR="$OUTPUTDIR",LOGFILE="$OUTPUTDIR/transfer_$DATE.log" wrapper_transfer.sh
     INPUTFILE="$OUTPUTDIR/$SAMPLE.bam"
 fi
 
 # Launch ExpansionHunter
 mkdir -p "$OUTPUTDIR/eh"
-qsub -pe smp 4 -q "$COMPUTE_QUEUE"  -N "eh_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/eh/$SAMPLE",LOGFILE="$OUTPUTDIR/eh/$DATE.log" "$(dirname "$0")/wrapper_expansionhunter.sh"
+qsub -wd "$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
 
 # Launch Tredparse
 mkdir -p "$OUTPUTDIR/tredparse"
-qsub -pe smp 4 -q "$COMPUTE_QUEUE" -N "tredparse_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTDIR="$OUTPUTDIR/tredparse",LOGFILE="$OUTPUTDIR/tredparse/$DATE.log" "$(dirname "$0")/wrapper_tredparse.sh"
+qsub -wd "$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
 
 # Launch GangSTR
 mkdir -p "$OUTPUTDIR/gangstr"
-qsub -pe smp 4 -q "$COMPUTE_QUEUE" -N "gangstr_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/gangstr/$SAMPLE",LOGFILE="$OUTPUTDIR/gangstr/$DATE.log" "$(dirname "$0")/wrapper_gangstr.sh"
+qsub -wd "$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
 
 # Launch ehdn profile
 mkdir -p "$OUTPUTDIR/ehdn"
-qsub -pe smp 4 -q "$COMPUTE_QUEUE" -N "ehdn_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" "$(dirname "$0")/wrapper_ehdn_profile.sh"
+qsub -wd "$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
 
 # Delete transfered bam and bai
 if [ "x$TRANSFER" = "xyes" ]
 then
-    qsub -pe smp 1 -q "$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" "$(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 -v SAMPLE="$SAMPLE",LOGFILE="$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."
 fi

pipeline_ehdn_outlier.sh

@@ -11,5 +11,5 @@
 
 CASE="$1"
 
-qsub -pe smp 1 -q "$COMPUTE_QUEUE" -N "ehdn_outlier_$CASE" -sync y -v CASE="$CASE" "$(dirname "$0")/wrapper_ehdn_outlier.sh"
+qsub -wd "$(dirname "$(readlink -f "$0")")" -pe smp 1 -q "$COMPUTE_QUEUE" -N "ehdn_outlier_$CASE" -sync y -v CASE="$CASE" wrapper_ehdn_outlier.sh
 

wrapper_delete.sh

@@ -8,7 +8,7 @@
 ## Usage: qsub -pe smp 1 -v SAMPLE=<sample>,[LOGFILE=<path to the log file>] wrapper_delete.sh
 
 # Source the configuration file
-. "$(dirname "$0")/config.sh"
+. ./config.sh
 
 # Log file path option
 if [ -z "$LOGFILE" ]

wrapper_ehdn_outlier.sh

@@ -7,7 +7,7 @@
 ## Description: script to generate automatically a manifest and multisampleprofile in a tsv format, then do outlier analyses for a single patient
 
 # Source the configuration file
-. "$(dirname "$0")/config.sh"
+. ./config.sh
 
 # Logging
 LOGFILE="$OUTPUTDIR/$CASE/ehdn/$CASE.ehdn_outlier.$(date +"%F_%H-%M-%S").log"

wrapper_ehdn_profile.sh

@@ -8,7 +8,7 @@
 ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_ehdn_profile.sh
 
 # Source the configuration file
-. "$(dirname "$0")/config.sh"
+. ./config.sh
 
 # Log file path option
 if [ -z "$LOGFILE" ]

wrapper_expansionhunter.sh

@@ -8,7 +8,8 @@
 ## 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
-. "$(dirname "$0")/config.sh"
+
+. ./config.sh
 
 # Log file path option
 if [ -z "$LOGFILE" ]

wrapper_gangstr.sh

@@ -8,7 +8,7 @@
 ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_gangstr.sh
 
 # Source the configuration file
-. "$(dirname "$0")/config.sh"
+. ./config.sh
 
 # Log file path option
 if [ -z "$LOGFILE" ]

wrapper_transfer.sh

@@ -5,7 +5,7 @@
 ## Licence: AGPLv3
 ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
 ## 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
 
 
 # Log file path option
@@ -28,7 +28,7 @@ then
 fi
 
 # Check if output directory is specified
-if [ -z "$OUTPUTDIR" ]
+if [ -z "$TRANSFER_OUTPUTDIR" ]
 then
     echo "Output directory is not specified"
     echo "$(date +"%F_%H-%M-%S"): END"
@@ -36,12 +36,12 @@ then
 fi
 
 # Transfer and check exit code
-echo "command : rsync -aAX \
+echo "command : rsync -aX \
     $INPUTFILE $(echo "$INPUTFILE" | sed 's/\.bam$/.bai/') \
-    $OUTPUTDIR"
-rsync -aAX \
+    $TRANSFER_OUTPUTDIR"
+rsync -aX \
     "$INPUTFILE" "$(echo "$INPUTFILE" | sed 's/\.bam$/.bai/')" \
-    "$OUTPUTDIR"
+    "$TRANSFER_OUTPUTDIR"
 
 transfer_exitcode=$? 
 

wrapper_tredparse.sh

@@ -5,10 +5,10 @@
 ## Licence: AGPLv3
 ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
 ## 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
 
 # Source the configuration file
-. "$(dirname "$0")/config.sh"
+. ./config.sh
 
 # Log file path option
 if [ -z "$LOGFILE" ]
@@ -30,7 +30,7 @@ then
 fi
 
 # Check if output prefix is specified
-if [ -z "$OUTPUTDIR" ]
+if [ -z "$TREDPARSE_OUTPUTDIR" ]
 then
     echo "Output directory is not specified"
     echo "$(date +"%F_%H-%M-%S"): END"
@@ -44,8 +44,8 @@ then
 fi
 
 # Launch script command and check exit code
-echo "command : $TREDPARSE $INPUTFILE --workdir $OUTPUTDIR --ref hg19"
-"$TREDPARSE" "$INPUTFILE" --workdir "$OUTPUTDIR" --ref hg19
+echo "command : $TREDPARSE $INPUTFILE --workdir $TREDPARSE_OUTPUTDIR --ref hg19"
+"$TREDPARSE" "$INPUTFILE" --workdir "$TREDPARSE_OUTPUTDIR" --ref hg19
 
 tredparse_exitcode=$?