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Anne-Sophie Denommé-Pichon
STR
Commits
2db647fe
Commit
2db647fe
authored
Nov 04, 2019
by
Anne-Sophie Denommé-Pichon
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#! /bin/sh
### ASDP PIPELINE ###
## wrapper_gangstr.sh
## Version : 0.0.1
## Licence : FIXME
## Description : a wrapper for qsubing GangSTR 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_gangstr.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104
## last revision date : 20191104
## Known bugs : None
# Log file path option
if
[
-z
"
$LOGFILE
"
]
then
LOGFILE
=
gangstr.
$(
date
+
"%F_%H-%M-%S"
)
.log
fi
# Logging
exec
1>>
"
$LOGFILE
"
2>&1
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: START"
# Check if input file exists
if
[
!
-f
"
$INPUTFILE
"
]
then
echo
"Input file '
$INPUTFILE
' does not exist"
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
gangstr.failed
exit
1
fi
# Check if output prefix is specified
if
[
-z
"
$OUTPUTPREFIX
"
]
then
echo
"Output prefix is not specified"
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
gangstr.failed
exit
1
fi
# Launch script command and check exit code
echo
"command : /work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR
\
--bam "
$INPUTFILE
"
\
--ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
--regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed
\
--out "
$OUTPUTPREFIX
"
\
--verbose"
/work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR
\
--bam
"
$INPUTFILE
"
\
--ref
/work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
--regions
/work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed
\
--out
"
$OUTPUTPREFIX
"
\
--verbose
gangstr_exitcode
=
$?
echo
"gangstr exit code :
$gangstr_exitcode
"
if
[
$gangstr_exitcode
!=
0
]
then
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
touch
gangstr.failed
exit
1
fi
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
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