Change the output prefix and add time stamp in the name

.gitignore

 *~
 *.bam
 *.bai
+*.vcf
+*.json
 *.sh.o*
 *.sh.po*
 *.failed

launch_expansionhunter.sh

@@ -15,7 +15,7 @@
 ## Known bugs : None
 
 INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
-OUTPUTPREFIX=test
+OUTPUTPREFIX=/user1/gad/an1770de/Tools/ExpansionHunter/20191102/"$(date +"%F_%H-%M-%S")"
 LOGFILE=/user1/gad/an1770de/Tools/ExpansionHunter/20191102/log.log
 
 # Launch the script on local host with --local option and on SGE with qsub without the --local option

wrapper_expansionhunter.sh

@@ -64,7 +64,7 @@ echo "command : /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linu
 expansionhunter_exitcode=$?
 
 # Remove .bam and .bai symbolic links
-rm "$TMPDIR/$(basenam e"$INPUTFILE")"
+rm "$TMPDIR/$(basename "$INPUTFILE")"
 rm "$TMPDIR/$(basename "$INPUTFILE").bai"
 rmdir "$TMPDIR"