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Anne-Sophie Denommé-Pichon
STR
Commits
fa20a9b3
Commit
fa20a9b3
authored
Jun 07, 2020
by
Anne-Sophie Denommé-Pichon
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Add variables to make scripts more generic
parent
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9 changed files
with
114 additions
and
80 deletions
+114
-80
README.md
README.md
+6
-7
launch_pipeline.sh
launch_pipeline.sh
+26
-16
pipeline.sh
pipeline.sh
+11
-8
wrapper_delete.sh
wrapper_delete.sh
+4
-2
wrapper_ehdn.sh
wrapper_ehdn.sh
+15
-7
wrapper_ehdn_outlier.sh
wrapper_ehdn_outlier.sh
+14
-17
wrapper_expansionhunter.sh
wrapper_expansionhunter.sh
+17
-9
wrapper_gangstr.sh
wrapper_gangstr.sh
+12
-9
wrapper_tredparse.sh
wrapper_tredparse.sh
+9
-5
No files found.
README.md
View file @
fa20a9b3
...
...
@@ -3,13 +3,13 @@
-
ASDP PIPELINE
-
Author: anne-sophie.denomme-pichon@u-bourgogne.fr
-
Version: 0.0.1
-
Licence:
FIXME
-
Licence:
AGPLv3
-
Description: How to launch scripts to get STR genotype from genomes on all the locus tested
1.
Create
`
genom
es.list`
2.
Specify output file in
`launch_pipeline
.sh`
. Warning, don't overwrite existing files
3.
Launch
`launch_pipeline.sh`
:
`nohup ./launch_pipeline.sh &`
. Dependencies
:
-
`
genom
es.list`
1.
Create
`
sampl
es.list`
2.
Fill the configuration file
`config
.sh`
. Warning, don't overwrite existing files
3.
Launch
`launch_pipeline.sh`
:
`nohup ./launch_pipeline.sh samples.list &`
. Dependencies
:
-
`
sampl
es.list`
-
`pipeline.sh`
-
`wrapper_delete.sh`
-
`wrapper_ehdn.sh`
...
...
@@ -23,4 +23,4 @@
7.
Specify input directory in
`triplets_outliers.py`
and in
`launch_triplets_outliers.sh`
.
8.
Change z-score threshold if necessary in
`triplets_outliers.py`
.
9.
Launch
`launch_triplets_outliers.sh`
. Dependency:
`patho.csv`
.
10.
Get files (i.e.:
`scp 'an1770de@ssh-ccub.u-bourgogne.fr:/work/gad/shared/analyse/STR/results/*' .`
)
\ No newline at end of file
10.
Get files (i.e.:
`scp 'an1770de@ssh-ccub.u-bourgogne.fr:/work/gad/shared/analyse/STR/results/*' .`
)
launch_pipeline.sh
View file @
fa20a9b3
#! /bin/sh
### ASDP PIPELINE ###
## launch_pipeline.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the pipeline for STR detection
## Usage :
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191208
## last revision date : 20200215
## Known bugs : None
/work/gad/shared/bin/parallel/parallel-20150522-1.el7.cern/bin/parallel
\
--jobs
16
\
## Version: 0.0.1
## Licence: AGPLV3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: script to launch the pipeline for STR detection. Receive multiple samples: one sample per line
# $1 : first argument in the command line : a list containing one sample per line, for exemple samples.list
SAMPLES
=
"
$1
"
# Check if sample is specified
if
[
-z
"
$SAMPLES
"
]
then
echo
"List of samples is not specified"
echo
"
$(
date
+
"%F_%H-%M-%S"
)
: END"
exit
1
fi
# Source configuration file
.
"
$(
dirname
"
$0
"
)
/config.sh"
# Parallel allow to parallelize the processing of multiple samples
"
$PARALLEL
"
\
--jobs
"
$PARALLEL_JOB_COUNT
"
\
--line-buffer
\
"
$(
dirname
"
$0
"
)
/pipeline.sh"
\
< genomes.list
<
"
$SAMPLES
"
pipeline.sh
View file @
fa20a9b3
...
...
@@ -18,31 +18,34 @@ then
exit
1
fi
INPUTFILE
=
"/archive/gad/shared/bam_new_genome_temp/
$SAMPLE
.bam"
# Source the configuration file
.
"
$(
dirname
"
$0
"
)
/config.sh"
INPUTFILE
=
"INPUTDIR/
$SAMPLE
.bam"
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
OUTPUTDIR
=
"
/work/gad/shared/analyse/STR/pipeline
/
$SAMPLE
"
OUTPUTDIR
=
"
OUTPUTDIR
/
$SAMPLE
"
# Transfer bam and bai from archive to work
mkdir
-p
"
$OUTPUTDIR
"
qsub
-pe
smp 1
-q
transfer
-N
"transfer_
$SAMPLE
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTDIR
=
"
$OUTPUTDIR
"
,LOGFILE
=
"
$OUTPUTDIR
/transfer_
$DATE
.log"
wrapper_transfer.sh
qsub
-pe
smp 1
-q
"
$TRANSFERQUEUE
"
-N
"transfer_
$SAMPLE
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTDIR
=
"
$OUTPUTDIR
"
,LOGFILE
=
"
$OUTPUTDIR
/transfer_
$DATE
.log"
wrapper_transfer.sh
INPUTFILE
=
"
$OUTPUTDIR
/
$SAMPLE
.bam"
# Launch ExpansionHunter
mkdir
-p
"
$OUTPUTDIR
/eh"
qsub
-pe
smp 4
-q
batch
-N
"eh_
$SAMPLE
"
-hold_jid
"transfer_
$SAMPLE
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTDIR
/eh/
$SAMPLE
"
,LOGFILE
=
"
$OUTPUTDIR
/eh/
$DATE
.log"
wrapper_expansionhunter.sh
qsub
-pe
smp 4
-q
"
$COMPUTEQUEUE
"
-N
"eh_
$SAMPLE
"
-hold_jid
"transfer_
$SAMPLE
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTDIR
/eh/
$SAMPLE
"
,LOGFILE
=
"
$OUTPUTDIR
/eh/
$DATE
.log"
wrapper_expansionhunter.sh
# Launch Tredparse
mkdir
-p
"
$OUTPUTDIR
/tredparse"
qsub
-pe
smp 4
-q
batch
-N
"tredparse_
$SAMPLE
"
-hold_jid
"transfer_
$SAMPLE
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTDIR
=
"
$OUTPUTDIR
/tredparse"
,LOGFILE
=
"
$OUTPUTDIR
/tredparse/
$DATE
.log"
wrapper_tredparse.sh
qsub
-pe
smp 4
-q
"
$COMPUTEQUEUE
"
-N
"tredparse_
$SAMPLE
"
-hold_jid
"transfer_
$SAMPLE
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTDIR
=
"
$OUTPUTDIR
/tredparse"
,LOGFILE
=
"
$OUTPUTDIR
/tredparse/
$DATE
.log"
wrapper_tredparse.sh
# Launch GangSTR
mkdir
-p
"
$OUTPUTDIR
/gangstr"
qsub
-pe
smp 4
-q
batch
-N
"gangstr_
$SAMPLE
"
-hold_jid
"transfer_
$SAMPLE
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTDIR
/gangstr/
$SAMPLE
"
,LOGFILE
=
"
$OUTPUTDIR
/gangstr/
$DATE
.log"
wrapper_gangstr.sh
qsub
-pe
smp 4
-q
"
$COMPUTEQUEUE
"
-N
"gangstr_
$SAMPLE
"
-hold_jid
"transfer_
$SAMPLE
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTDIR
/gangstr/
$SAMPLE
"
,LOGFILE
=
"
$OUTPUTDIR
/gangstr/
$DATE
.log"
wrapper_gangstr.sh
# Launch ehdn profile
mkdir
-p
"
$OUTPUTDIR
/ehdn"
qsub
-pe
smp 4
-q
batch
-N
"ehdn_
$SAMPLE
"
-hold_jid
"transfer_
$SAMPLE
"
-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_
$SAMPLE
"
-v
INPUTFILE
=
"
$INPUTFILE
"
,OUTPUTPREFIX
=
"
$OUTPUTDIR
/ehdn/
$SAMPLE
"
,LOGFILE
=
"
$OUTPUTDIR
/ehdn/
$DATE
.log"
wrapper_ehdn.sh
# Delete transfered bam and bai
qsub
-pe
smp 1
-q
batch
-N
"delete_
$SAMPLE
"
-hold_jid
"eh_
$SAMPLE
,tredparse_
$SAMPLE
,gangstr_
$SAMPLE
,ehdn_
$SAMPLE
"
-sync
y
-v
SAMPLE
=
"
$SAMPLE
"
,LOGFILE
=
"
$OUTPUTDIR
/delete_
$DATE
.log"
wrapper_delete.sh
qsub
-pe
smp 1
-q
"
$COMPUTEQUEUE
"
-N
"delete_
$SAMPLE
"
-hold_jid
"eh_
$SAMPLE
,tredparse_
$SAMPLE
,gangstr_
$SAMPLE
,ehdn_
$SAMPLE
"
-sync
y
-v
SAMPLE
=
"
$SAMPLE
"
,LOGFILE
=
"
$OUTPUTDIR
/delete_
$DATE
.log"
wrapper_delete.sh
wrapper_delete.sh
View file @
fa20a9b3
...
...
@@ -7,6 +7,8 @@
## Description: a wrapper for qsubing bam deletion for STR pipeline
## Usage: qsub -pe smp 1 -v SAMPLE=<sample>,[LOGFILE=<path to the log file>] wrapper_delete.sh
# Source the configuration file
.
"
$(
dirname
"
$0
"
)
/config.sh"
# Log file path option
if
[
-z
"
$LOGFILE
"
]
...
...
@@ -30,8 +32,8 @@ fi
echo
"command : rm
\
$SAMPLE
"
rm
\
"
/work/gad/shared/analyse/STR/pipeline
/
$SAMPLE
/
$SAMPLE
.bam"
\
"
/work/gad/shared/analyse/STR/pipeline
/
$SAMPLE
/
$SAMPLE
.bai"
"
$OUTPUTDIR
/
$SAMPLE
/
$SAMPLE
.bam"
\
"
$OUTPUTDIR
/
$SAMPLE
/
$SAMPLE
.bai"
delete_exitcode
=
$?
...
...
wrapper_ehdn.sh
View file @
fa20a9b3
...
...
@@ -7,6 +7,8 @@
## 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
# Source the configuration file
.
"
$(
dirname
"
$0
"
)
/config.sh"
# Log file path option
if
[
-z
"
$LOGFILE
"
]
...
...
@@ -35,21 +37,27 @@ then
exit
1
fi
# Create .bam and .bai symbolic links
# Create .bam and .bai symbolic links
(EHDN expects .bam.bai)
TMPDIR
=
"
$(
mktemp
-d
)
"
ln
-s
"
$INPUTFILE
"
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
"
ln
-s
"
$(
echo
"
$INPUTFILE
"
|
sed
's/\.bam$/.bai/'
)
"
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
.bai"
if
[
-f
"
$INPUTFILE
.bai"
]
then
ln
-s
"
$INPUTFILE
.bai"
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
.bai"
else
ln
-s
"
$(
echo
"
$INPUTFILE
"
|
sed
's/\.bam$/.bai/'
)
"
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
.bai"
fi
# Launch script command and check exit code
echo
"command :
/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0
profile
\
--reads
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
"
\
--reference
/work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
echo
"command :
$EHDN
profile
\
--reads
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
\
--reference
$REF
\
--output-prefix
$OUTPUTPREFIX
\
--min-anchor-mapq 50
\
--max-irr-mapq 40"
/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0 profile
\
"
$EHDN
"
profile
\
--reads
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
"
\
--reference
/work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
--reference
"
$REF
"
\
--output-prefix
"
$OUTPUTPREFIX
"
\
--min-anchor-mapq
50
\
--max-irr-mapq
40
...
...
wrapper_ehdn_outlier.sh
View file @
fa20a9b3
...
...
@@ -6,11 +6,8 @@
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: script to generate automatically a manifest and multisampleprofile in a tsv format, then do outlier analyses for a single patient
EHDN
=
"/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/bin/ExpansionHunterDenovo-v0.8.0"
EHDN_OUTLIER
=
"/work/gad/shared/bin/expansionhunterdenovo/ExpansionHunterDenovo-v0.8.0-linux_x86_64/scripts/outlier.py"
REFERENCE
=
"/work/gad/shared/pipeline/hg19/index/hg19_essential.fa"
WORKDIR
=
"/work/gad/shared/analyse/STR/pipeline"
# Source the configuration file
.
"
$(
dirname
"
$0
"
)
/config.sh"
# Log file path option
if
[
-z
"
$LOGFILE
"
]
...
...
@@ -31,20 +28,20 @@ then
fi
# Generate manifest for one patient with all samples (to write lines in the file)
cd
"
$
WORK
DIR
"
cd
"
$
OUTPUT
DIR
"
for
dijen
in
dijen
*
do
# Check if str_profile.json exists
if
[
-f
"
$
WORK
DIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
]
if
[
-f
"
$
OUTPUT
DIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
]
then
if
[
"x
$dijen
"
=
"x
$CASE
"
]
then
echo
-e
"
$dijen
\t
case
\t
$
WORK
DIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
echo
-e
"
$dijen
\t
case
\t
$
OUTPUT
DIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
else
echo
-e
"
$dijen
\t
control
\t
$
WORK
DIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
echo
-e
"
$dijen
\t
control
\t
$
OUTPUT
DIR
/
$dijen
/ehdn/
$dijen
.str_profile.json"
fi
fi
done
>
"
$
WORK
DIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
done
>
"
$
OUTPUT
DIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
ehdn_outlier_exitcode
=
$?
...
...
@@ -58,7 +55,7 @@ fi
# Generate multisampleprofile for one patient with all samples
"
$EHDN
"
merge
\
--reference
"
$REFERENCE
"
\
--manifest
"
$
WORK
DIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--manifest
"
$
OUTPUT
DIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--output-prefix
"
$CASE
/ehdn/
$CASE
"
ehdn_outlier_exitcode
=
$?
...
...
@@ -72,9 +69,9 @@ fi
# Run locus-based comparison analysis
"
$EHDN_OUTLIER
"
locus
\
--manifest
"
$
WORK
DIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$
WORK
DIR
/
$CASE
/ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$
WORK
DIR
/
$CASE
/ehdn/
$CASE
.outlier_locus.tsv"
--manifest
"
$
OUTPUT
DIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$
OUTPUT
DIR
/
$CASE
/ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$
OUTPUT
DIR
/
$CASE
/ehdn/
$CASE
.outlier_locus.tsv"
ehdn_outlier_exitcode
=
$?
...
...
@@ -88,9 +85,9 @@ fi
# Run motif_based comparison analysis
"
$EHDN_OUTLIER
"
motif
\
--manifest
"
$
WORK
DIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$
WORK
DIR
/
$CASE
/ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$
WORK
DIR
/
$CASE
/ehdn/
$CASE
.outlier_motif.tsv"
--manifest
"
$
OUTPUT
DIR
/
$CASE
/ehdn/
$CASE
.manifest.tsv"
\
--multisample-profile
"
$
OUTPUT
DIR
/
$CASE
/ehdn/
$CASE
.multisample_profile.json"
\
--output
"
$
OUTPUT
DIR
/
$CASE
/ehdn/
$CASE
.outlier_motif.tsv"
ehdn_outlier_exitcode
=
$?
...
...
wrapper_expansionhunter.sh
View file @
fa20a9b3
...
...
@@ -7,6 +7,8 @@
## Description: a wrapper for qsubing ExpansionHunter 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_expansionhunter.sh
# Source the configuration file
.
"
$(
dirname
"
$0
"
)
/config.sh"
# Log file path option
if
[
-z
"
$LOGFILE
"
]
...
...
@@ -35,21 +37,27 @@ then
exit
1
fi
# Create .bam and .bai symbolic links
# Create .bam and .bai symbolic links
(EH expects .bam.bai)
TMPDIR
=
"
$(
mktemp
-d
)
"
ln
-s
"
$INPUTFILE
"
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
"
ln
-s
"
$(
echo
"
$INPUTFILE
"
|
sed
's/\.bam$/.bai/'
)
"
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
.bai"
if
[
-f
"
$INPUTFILE
.bai"
]
then
ln
-s
"
$INPUTFILE
.bai"
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
.bai"
else
ln
-s
"
$(
echo
"
$INPUTFILE
"
|
sed
's/\.bam$/.bai/'
)
"
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
.bai"
fi
# Launch script command and check exit code
echo
"command :
/work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter
\
--reads
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
"
\
--reference
/work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
--variant-catalog
/work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json
\
echo
"command :
$EH
\
--reads
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
\
--reference
$REF
\
--variant-catalog
$EH_VARIANT_CATALOG
\
--output-prefix
$OUTPUTPREFIX
"
/work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/bin/ExpansionHunter
\
"
$EH
"
\
--reads
"
$TMPDIR
/
$(
basename
"
$INPUTFILE
"
)
"
\
--reference
/work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
--variant-catalog
/work/gad/shared/bin/expansionhunter/ExpansionHunter-v3.1.2-linux_x86_64/variant_catalog/hg19/variant_catalog.json
\
--reference
"
$REF
"
\
--variant-catalog
"
$EH_VARIANT_CATALOG
"
\
--output-prefix
"
$OUTPUTPREFIX
"
expansionhunter_exitcode
=
$?
...
...
wrapper_gangstr.sh
View file @
fa20a9b3
...
...
@@ -7,6 +7,9 @@
## 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
# Source the configuration file
.
"
$(
dirname
"
$0
"
)
/config.sh"
# Log file path option
if
[
-z
"
$LOGFILE
"
]
then
...
...
@@ -35,20 +38,20 @@ then
fi
# Launch script command and check exit code
echo
"command :
/work/gad/shared/bin/gangstr/GangSTR-2.4/bin/Gang
STR
\
--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
echo
"command :
$GANG
STR
\
--bam
$INPUTFILE
\
--ref
$REF
\
--regions
$GANGSTR_REGIONS
\
--out
$OUTPUTPREFIX
\
--verbose
"
# --insertmean "$INSERTMEAN" \
# --insertsdev "$INSERTDEV""
/work/gad/shared/bin/gangstr/GangSTR-2.4/bin/GangSTR
\
"
$GANGSTR
"
\
--bam
"
$INPUTFILE
"
\
--ref
/work/gad/shared/pipeline/hg19/index/hg19_essential.fa
\
--regions
/work/gad/shared/bin/gangstr/STRregions/hg19_ver13_1.bed
\
--ref
"
$REF
"
\
--regions
"
$GANGSTR_REGIONS
"
\
--out
"
$OUTPUTPREFIX
"
\
--verbose
...
...
wrapper_tredparse.sh
View file @
fa20a9b3
...
...
@@ -7,6 +7,8 @@
## Description: a wrapper for qsubing Tredparse script for STR detection
## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_tredparse.sh
# Source the configuration file
.
"
$(
dirname
"
$0
"
)
/config.sh"
# Log file path option
if
[
-z
"
$LOGFILE
"
]
...
...
@@ -35,13 +37,15 @@ then
exit
1
fi
# Enable the virtualenv
TREDPARSE
=
"/work/gad/shared/bin/tredparse/Tredparse-20190901"
.
"
$TREDPARSE
/bin/activate"
# Enable the virtualenv if any
if
[
-n
"
$TREDPARSE_VENV
"
]
then
.
"
$TREDPARSE_VENV
"
fi
# Launch script command and check exit code
echo
"command :
"
$TREDPARSE
/bin/tred.py
" "
$INPUTFILE
" --workdir "
$OUTPUTDIR
"
--ref hg19"
"
$TREDPARSE
/bin/tred.py
"
"
$INPUTFILE
"
--workdir
"
$OUTPUTDIR
"
--ref
hg19
echo
"command :
$TREDPARSE
$INPUTFILE
--workdir
$OUTPUTDIR
--ref hg19"
"
$TREDPARSE
"
"
$INPUTFILE
"
--workdir
"
$OUTPUTDIR
"
--ref
hg19
tredparse_exitcode
=
$?
...
...
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