Rename wrapper_ehdn.sh to wrapper_ehdn_profile.sh

README.md

@@ -14,7 +14,7 @@
    - `wrapper_delete.sh`
    - `wrapper_ehdn.sh`
    - `wrapper_expansionhunter.sh`
-   - `wrapper_gangstre.sh`
+   - `wrapper_gangstr.sh`
    - `wrapper_transfer.sh`
    - `wrapper_tredparse.sh`
 4. Launch `getResults.py`. Warning, don't overwrite existing files.

launch_ehdn.sh → launch_ehdn_profile.sh

@@ -17,8 +17,8 @@ LOGFILE="$OUTPUTDIR/$DATE.log"
 if [ $# -eq 1 ] && [ "x$1" = x--local ]
 then
     mkdir -p "$OUTPUTDIR"
-    INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn.sh"
+    INPUTFILE="$INPUTFILE" OUTPUTPREFIX="$OUTPUTPREFIX" LOGFILE="$LOGFILE" "$(dirname "$0")/wrapper_ehdn_profile.sh"
 else 
     mkdir -p "$OUTPUTDIR"
-    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_ehdn.sh
+    qsub -pe smp 4 -q batch -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTPREFIX",LOGFILE="$LOGFILE" wrapper_ehdn_profile.sh
 fi

pipeline.sh

@@ -55,7 +55,7 @@ qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "gangstr_$SAMPLE" -hold_jid "$TRANSFER_JOB"
 
 # Launch ehdn profile
 mkdir -p "$OUTPUTDIR/ehdn"
-qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "ehdn_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn.sh
+qsub -pe smp 4 -q "$COMPUTEQUEUE" -N "ehdn_$SAMPLE" -hold_jid "$TRANSFER_JOB" -v INPUTFILE="$INPUTFILE",OUTPUTPREFIX="$OUTPUTDIR/ehdn/$SAMPLE",LOGFILE="$OUTPUTDIR/ehdn/$DATE.log" wrapper_ehdn_profile.sh
 
 # Delete transfered bam and bai
 if [ "x$TRANSFER" = "xyes" ]

wrapper_ehdn.sh → wrapper_ehdn_profile.sh

@@ -5,7 +5,7 @@
 ## Licence: AGPLv3
 ## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
 ## Description: a wrapper for qsubing ExpansionHunter denovo script for STR detection
-## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTPREFIX=<output prefix>,[LOGFILE=<path to the log file>] wrapper_ehdn.sh
+## 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"