Change the output prefix and add time stamp in the name

parent 776de494
*~ *~
*.bam *.bam
*.bai *.bai
*.vcf
*.json
*.sh.o* *.sh.o*
*.sh.po* *.sh.po*
*.failed *.failed
......
...@@ -15,7 +15,7 @@ ...@@ -15,7 +15,7 @@
## Known bugs : None ## Known bugs : None
INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam INPUTFILE=/archive/gad/shared/bam_new_genome_temp/dijen017.bam
OUTPUTPREFIX=test OUTPUTPREFIX=/user1/gad/an1770de/Tools/ExpansionHunter/20191102/"$(date +"%F_%H-%M-%S")"
LOGFILE=/user1/gad/an1770de/Tools/ExpansionHunter/20191102/log.log LOGFILE=/user1/gad/an1770de/Tools/ExpansionHunter/20191102/log.log
# Launch the script on local host with --local option and on SGE with qsub without the --local option # Launch the script on local host with --local option and on SGE with qsub without the --local option
......
...@@ -64,7 +64,7 @@ echo "command : /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linu ...@@ -64,7 +64,7 @@ echo "command : /work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linu
expansionhunter_exitcode=$? expansionhunter_exitcode=$?
# Remove .bam and .bai symbolic links # Remove .bam and .bai symbolic links
rm "$TMPDIR/$(basenam e"$INPUTFILE")" rm "$TMPDIR/$(basename "$INPUTFILE")"
rm "$TMPDIR/$(basename "$INPUTFILE").bai" rm "$TMPDIR/$(basename "$INPUTFILE").bai"
rmdir "$TMPDIR" rmdir "$TMPDIR"
......
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