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Anne-Sophie Denommé-Pichon
STR
Commits
14be1720
Commit
14be1720
authored
Jun 06, 2020
by
Anne-Sophie Denommé-Pichon
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16 changed files
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67 additions
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172 deletions
+67
-172
launch_ehdn.sh
launch_ehdn.sh
+4
-11
launch_ehdn_outlier.sh
launch_ehdn_outlier.sh
+2
-8
launch_expansionhunter.sh
launch_expansionhunter.sh
+4
-11
launch_gangstr.sh
launch_gangstr.sh
+4
-11
launch_pipeline_ehdn.sh
launch_pipeline_ehdn.sh
+2
-8
launch_transfer.sh
launch_transfer.sh
+4
-11
launch_tredparse.sh
launch_tredparse.sh
+5
-11
pipeline.sh
pipeline.sh
+5
-8
wrapper_delete.sh
wrapper_delete.sh
+5
-12
wrapper_ehdn.sh
wrapper_ehdn.sh
+5
-12
wrapper_ehdn_outlier.sh
wrapper_ehdn_outlier.sh
+2
-8
wrapper_expansionhunter.sh
wrapper_expansionhunter.sh
+5
-12
wrapper_gangstr.sh
wrapper_gangstr.sh
+5
-13
wrapper_stretch.sh
wrapper_stretch.sh
+5
-12
wrapper_transfer.sh
wrapper_transfer.sh
+5
-12
wrapper_tredparse.sh
wrapper_tredparse.sh
+5
-12
No files found.
launch_ehdn.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_ehdn.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing ExpansionHunter denovo script for STR detection
## Usage :
## Output : FIXME
## Requirements : FIXME
## Version: 0.0.1
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: script to launch the wrapper for qsubing ExpansionHunter denovo script for STR detection
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102
## last revision date : 20191126
## Known bugs : None
INPUTFILE
=
/work/gad/shared/analyse/STR/pipeline/dijen073/dijen073.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
...
...
launch_ehdn_outlier.sh
View file @
14be1720
...
...
@@ -2,16 +2,10 @@
### ASDP PIPELINE ###
## Version: 0.0.1
## Licence: FIXME
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: script to launch the wrapper for qsubing outlier analysis by ExpansionHunter denovo script for STR detection
## Usage: FIXME
## Output: FIXME
## Requirements: FIXME
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date: 20200215
## Last revision date: 20200215
## Known bugs: None
CASE
=
"
$1
"
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
...
...
launch_expansionhunter.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_expansionhunter.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing ExpansionHunter script for STR detection
## Usage :
## Output : FIXME
## Requirements : FIXME
## Version: 0.0.1
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: script to launch the wrapper for qsubing ExpansionHunter script for STR detection
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102
## last revision date : 20191126
## Known bugs : None
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen561.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
...
...
launch_gangstr.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_gangstr.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing GangSTR script for STR detection
## Usage : FIXME
## Output : FIXME
## Requirements : FIXME
## Version: 0.0.1
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: script to launch the wrapper for qsubing GangSTR script for STR detection
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191104
## last revision date : 20191126
## Known bugs : None
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen017/offtargetdijen017/dijen017.offtarget.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
...
...
launch_pipeline_ehdn.sh
View file @
14be1720
...
...
@@ -2,16 +2,10 @@
### ASDP PIPELINE ###
## Version: 0.0.1
## Licence: FIXME
## Licence: AGPLv3
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Description : script to launch the pipeline for STR detection with EHDN outlier
## Usage :
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20200215
## last revision date : 20200215
## Known bugs : None
LAUNCHER
=
"
$(
readlink
-f
"
$(
dirname
"
$0
"
)
/launch_ehdn_outlier.sh"
)
"
...
...
launch_transfer.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_transfer.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing ExpansionHunter denovo script for STR detection
## Usage :
## Output : FIXME
## Requirements : FIXME
## Version: 0.0.1
## Licence: AGPLv3
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102
## last revision date : 20191126
## Known bugs : None
## Description: script to launch the wrapper for qsubing ExpansionHunter denovo script for STR detection
INPUTFILE
=
"/archive/gad/shared/bam_new_genome_temp/dijen016.bam"
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
...
...
launch_tredparse.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## launch_wrapper_tredparse.sh
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the wrapper for qsubing Tredparse script for STR detection
## Usage : FIXME
## Output : FIXME
## Requirements : FIXME
## Version: 0.0.1
## Licence: AGPLv3
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
##
Creation Date : 20191103
## last revision date : 20191126
## Known bugs : None
##
Description: script to launch the wrapper for qsubing Tredparse script for STR detection
INPUTFILE
=
/work/gad/shared/analyse/STR/Data/dijen561.bam
DATE
=
"
$(
date
+
"%F_%H-%M-%S"
)
"
...
...
pipeline.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## Version : 0.0.1
## Licence : FIXME
## Description : script to launch the pipeline for STR detection
## Usage :
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191208
## last revision date : 20200606
## Version: 0.0.1
## Licence: AGPLV3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: script to launch the pipeline for STR detection
# $1 : first argument in the command line : the input file
SAMPLE
=
"
$1
"
...
...
wrapper_delete.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_delete.sh
## Version : 0.0.1
## Licence : FIXME
## 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
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191208
## last revision date : 20191208
## Known bugs : None
## Version: 0.0.1
## Licence: AGPLV3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## 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
# Log file path option
...
...
wrapper_ehdn.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_ehdn.sh
## Version : 0.0.1
## Licence : FIXME
## 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
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191208
## last revision date : 20191208
## Known bugs : None
## Version: 0.0.1
## 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
# Log file path option
...
...
wrapper_ehdn_outlier.sh
View file @
14be1720
...
...
@@ -2,16 +2,10 @@
### ASDP PIPELINE ###
## Version: 0.0.1
## Licence: FIXME
## Licence: AGPLv3
## 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
## Usage: FIXME
## Output: FIXME
## Requirements: FIXME
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date: 20200215
## Last revision date: 20200215
## Known bugs: None
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"
...
...
wrapper_expansionhunter.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_expansionhunter.sh
## Version : 0.0.1
## Licence : FIXME
## 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
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191102
## last revision date : 20191102
## Known bugs : None
## Version: 0.0.1
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## 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
# Log file path option
...
...
wrapper_gangstr.sh
View file @
14be1720
#! /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 : 20191127
## Known bugs : None
## Version: 0.0.1
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## 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
# Log file path option
if
[
-z
"
$LOGFILE
"
]
...
...
wrapper_stretch.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_stretch.sh
## Version : 0.0.1
## Licence : FIXME
## Description : a wrapper for qsubing STRetch 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_stretch.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191118
## last revision date : 20191118
## Known bugs : None
## Version: 0.0.1
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: a wrapper for qsubing STRetch 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_stretch.sh
# Log file path option
...
...
wrapper_transfer.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_transfer.sh
## Version : 0.0.1
## Licence : FIXME
## Description : a wrapper for qsubing bam transfer for STR pipeline
## Usage : qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_transfer.sh
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191208
## last revision date : 20191208
## Known bugs : None
## Version: 0.0.1
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## Description: a wrapper for qsubing bam transfer for STR pipeline
## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_transfer.sh
# Log file path option
...
...
wrapper_tredparse.sh
View file @
14be1720
#! /bin/sh
### ASDP PIPELINE ###
## wrapper_tredparse.sh
## Version : 0.0.1
## Licence : FIXME
## 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
## Output : FIXME
## Requirements : FIXME
## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
## Creation Date : 20191103
## last revision date : 20191103
## Known bugs : None
## Version: 0.0.1
## Licence: AGPLv3
## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
## 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
# Log file path option
...
...
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