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Anne-Sophie Denommé-Pichon
STR
Commits
85802bc1
Commit
85802bc1
authored
Dec 08, 2019
by
Anne-Sophie Denommé-Pichon
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Update queue and add stretch wrapper
parent
5b438991
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Inline
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Showing
8 changed files
with
55 additions
and
18 deletions
+55
-18
launch_expansionhunter.sh
launch_expansionhunter.sh
+3
-3
launch_gangstr.sh
launch_gangstr.sh
+6
-4
launch_lobstr.sh
launch_lobstr.sh
+1
-1
launch_stretch.sh
launch_stretch.sh
+32
-0
launch_tredparse.sh
launch_tredparse.sh
+2
-2
wrapper_gangstr.sh
wrapper_gangstr.sh
+8
-3
wrapper_samtoolssortbyread.sh
wrapper_samtoolssortbyread.sh
+1
-1
wrapper_stretch.sh
wrapper_stretch.sh
+2
-4
No files found.
launch_expansionhunter.sh
View file @
85802bc1
...
...
@@ -11,10 +11,10 @@
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102
## last revision date : 201911
02
## last revision date : 201911
26
## Known bugs : None
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen017/
dijen017/dijen017
.bam
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen017/
offtargetdijen017/dijen017.offtarget
.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/ExpansionHunter/
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
"
...
...
@@ -27,5 +27,5 @@ then
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_expansionhunter.sh"
else
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp
1
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_expansionhunter.sh
qsub
-pe
smp
4
-q
batch
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_expansionhunter.sh
fi
launch_gangstr.sh
View file @
85802bc1
...
...
@@ -11,21 +11,23 @@
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104
## last revision date : 201911
17
## last revision date : 201911
26
## Known bugs : None
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen017/
dijen017/dijen017
.bam
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen017/
offtargetdijen017/dijen017.offtarget
.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/GangSTR/
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
"
LOGFILE
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
.log"
INSERTMEAN
=
"359.4"
INSERTDEV
=
"80.1204"
# Launch the script on local host with --local option and on SGE with qsub without the --local option
if
[
$#
-eq
1
]
&&
[
"x
$1
"
=
x--local
]
then
mkdir
-p
"
$OUTPUTDIR
"
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_gangstr.sh"
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
LOGFILE
=
"
$LOGFILE
"
INSERTMEAN
=
"
$INSERTMEAN
"
INSERTDEV
=
"
$INSERTDEV
"
"
$(
dirname
"
$0
"
)
/wrapper_gangstr.sh"
else
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp
1
-q
batch
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_gangstr.sh
qsub
-pe
smp
4
-q
batch
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTPREFIX
"
,LOGFILE
=
"
$LOGFILE
"
,INSERTMEAN
=
"
$INSERTMEAN
"
,INSERTDEV
=
"
$INSERTDEV
"
wrapper_gangstr.sh
fi
launch_lobstr.sh
View file @
85802bc1
...
...
@@ -14,7 +14,7 @@
## last revision date : 20191104
## Known bugs : None
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen017/
dijen017/dijen017
.bam
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen017/
lobSTR/2019-11-18/dijen017.sorted
.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/LobSTR/
$DATE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
"
...
...
launch_stretch.sh
0 → 100755
View file @
85802bc1
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_stretch.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing STRetch script for STR detection
## Usage : FIXME
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191118
## last revision date : 20191127
## Known bugs : None
# INPUTFILE=/work/gad/shared/analyse/STR/Data/dijen017/dijen017/dijen017.bam
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen017/shortdijen017/dijen017.short.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/STRetch/
$DATE
"
LOGFILE
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
.log"
# Launch the script on local host with --local option and on SGE with qsub without the --local option
if
[
$#
-eq
1
]
&&
[
"x
$1
"
=
x--local
]
then
mkdir
-p
"
$OUTPUTDIR
"
INPUTFILE
=
"
$INPUTFILE
"
OUTPUTPREFIX
=
"
$OUTPUTDIR
"
LOGFILE
=
"
$LOGFILE
"
"
$(
dirname
"
$0
"
)
/wrapper_stretch.sh"
else
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp 16
-q
batch
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTDIR
"
,LOGFILE
=
"
$LOGFILE
"
wrapper_stretch.sh
fi
launch_tredparse.sh
View file @
85802bc1
...
...
@@ -11,10 +11,10 @@
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191103
## last revision date : 201911
03
## last revision date : 201911
26
## Known bugs : None
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen017/
dijen017/dijen017
.bam
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen017/
offtargetdijen017/dijen017.offtarget
.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"/work/gad/shared/analyse/STR/Tredparse/
$DATE
"
LOGFILE
=
"
$OUTPUTDIR
/
$(
basename
"
$INPUTFILE
"
)
_
$DATE
.log"
...
...
wrapper_gangstr.sh
View file @
85802bc1
...
...
@@ -11,7 +11,7 @@
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104
## last revision date : 201911
04
## last revision date : 201911
27
## Known bugs : None
...
...
@@ -50,14 +50,19 @@ echo "command : /work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR \
--ref /work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
--regions /work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed
\
--out "
$OUTPUTPREFIX
"
\
--verbose"
--verbose
\
--insertmean "
$INSERTMEAN
"
\
--insertsdev "
$INSERTDEV
""
/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
--verbose
\
--insertmean
"
$INSERTMEAN
"
\
--insertsdev
"
$INSERTDEV
"
gangstr_exitcode
=
$?
...
...
wrapper_samtoolssortbyread.sh
View file @
85802bc1
#! /bin/sh
samtools
sort
-n
-@64
-
T
/work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-18
-o
/work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-18
/dijen017.sorted.bam /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/dijen017.bam
samtools
sort
-n
-@64
-
-check
=
quiet
-T
sortbyread /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-26
-o
/work/gad/shared/analyse/STR/Data/dijen017/lobSTR/2019-11-26
/dijen017.sorted.bam /work/gad/shared/analyse/STR/Data/dijen017/lobSTR/dijen017.bam
wrapper_stretch.sh
View file @
85802bc1
...
...
@@ -47,15 +47,13 @@ fi
# Launch script command and check exit code
echo
"cd "
$OUTPUTDIR
"
/work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe
\
run -p
\
input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed
\
run -p input_regions=/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed
\
/work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy
\
"
$INPUTFILE
""
cd
"
$OUTPUTDIR
"
/work/gad/shared/bin/stretch/STRetch-20190602/tools/bin/bpipe
\
run
-p
input_regions
=
/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed
\
run
-p
input_regions
=
/work/gad/shared/bin/stretch/STRetch-20190602/reference-data/hg19.STR_disease_loci.bed
\
/work/gad/shared/bin/stretch/STRetch-20190602/pipelines/STRetch_wgs_bam_pipeline.groovy
\
"
$INPUTFILE
"
...
...
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