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Anne-Sophie Denommé-Pichon
STR
Commits
b72da0c7
Commit
b72da0c7
authored
Jun 07, 2020
by
Anne-Sophie Denommé-Pichon
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Rename wrapper_ehdn.sh to wrapper_ehdn_profile.sh
parent
16f9d1ec
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4 changed files
with
5 additions
and
5 deletions
+5
-5
README.md
README.md
+1
-1
launch_ehdn_profile.sh
launch_ehdn_profile.sh
+2
-2
pipeline.sh
pipeline.sh
+1
-1
wrapper_ehdn_profile.sh
wrapper_ehdn_profile.sh
+1
-1
No files found.
README.md
View file @
b72da0c7
...
...
@@ -14,7 +14,7 @@
-
`wrapper_delete.sh`
-
`wrapper_ehdn.sh`
-
`wrapper_expansionhunter.sh`
-
`wrapper_gangstr
e
.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
View file @
b72da0c7
...
...
@@ -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
=
"
$LOGFILE
"
wrapper_ehdn
_profile
.sh
fi
pipeline.sh
View file @
b72da0c7
...
...
@@ -55,7 +55,7 @@ qsub -pe smp 4 -q "$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
View file @
b72da0c7
...
...
@@ -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"
...
...
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