Remove email address

README.md

 # STR detection pipeline
 
 - ASDP PIPELINE
-- Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+- Author:  Anne-Sophie Denommé-Pichon
 - Version: 0.0.1
 - Licence: AGPLv3
 - Description: How to launch scripts to get STR genotype from genomes on all the locus tested
@@ -32,5 +32,5 @@ For now, scripts have to be launched from the clone directory.
    - `launch_str_outliers.sh`
    - `str_outliers.py`
 6. Optional: launch `launch_str_plotly.sh`.
-7. Get files (i.e.: `scp 'an1770de@ssh-ccub.u-bourgogne.fr:/work/gad/shared/analyse/STR/results/*' .`)
+7. Get files (i.e.: `scp 'username@ssh-ccub.u-bourgogne.fr:/work/gad/shared/analyse/STR/results/*' .`)
 

config.sh

@@ -3,7 +3,7 @@
 ### ASDP pipeline###
 ## Version: 0.0.1
 ## License; AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## Description: configuration file
 
 INPUTDIR="/archive/gad/shared/bam_new_genome_temp"

getResults.py

@@ -4,7 +4,7 @@
 ## getResults.py
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## Description: script to get automatically results from pipeline.sh script in a tsv format on all the locus
 
 import csv

launch_pipeline.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLV3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## 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

launch_pipeline_ehdn_outlier.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author : Anne-Sophie Denommé-Pichon
 ## Description : script to launch the pipeline for STR detection with EHDN outlier
 
 # Source configuration file

launch_results.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLV3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## Description: script to launch the pipeline for getting STR detection results. 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

launch_str_outliers.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author : Anne-Sophie Denommé-Pichon
 ## Description : script to launch the script to get automatically outliers from expansion pipeline results from getResults.py
 
 # Source configuration file

launch_str_plotly.sh

@@ -3,7 +3,7 @@
 ### ASDP pipeline###
 ## Version: 0.0.1
 ## License; AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## Description: script to launch the script to get automatically graphics from expansion pipeline results from getResults.py with Plotly
 
 # Source configuration file

pipeline.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLV3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## Description: script to launch the pipeline for STR detection. This script handles a single sample.
 
 

pipeline_ehdn_outlier.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## Description: script to launch the wrapper for qsubing outlier analysis by ExpansionHunter denovo script for STR detection
 
 # Source configuration file

str_outliers.py

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version : 0.0.1
 ## Licence : AGPLv3
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author : Anne-Sophie Denommé-Pichon
 ## Description : script to get automatically outliers from expansion pipeline results from getResults.py
 
 

str_plotly.py

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author : anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author : Anne-Sophie Denommé-Pichon
 ## Description: script to get automatically graphics from expansion pipeline results from getResults.py with Plotly
 
 import collections

wrapper_delete.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLV3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## 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
 

wrapper_ehdn_outlier.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## Description: script to generate automatically a manifest and multisampleprofile in a tsv format, then do outlier analyses for a single patient
 
 # Source the configuration file

wrapper_ehdn_profile.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## 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_profile.sh
 

wrapper_expansionhunter.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## 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
 

wrapper_gangstr.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## 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
 

wrapper_transfer.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## Description: a wrapper for qsubing bam transfer for STR pipeline
 ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,TRANSFER_OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_transfer.sh
 

wrapper_tredparse.sh

@@ -3,7 +3,7 @@
 ### ASDP PIPELINE ###
 ## Version: 0.0.1
 ## Licence: AGPLv3
-## Author: anne-sophie.denomme-pichon@u-bourgogne.fr
+## Author: Anne-Sophie Denommé-Pichon
 ## Description: a wrapper for qsubing Tredparse script for STR detection
 ## Usage: qsub -pe smp 1 -v INPUTFILE=<path to the bam file>,TREDPARSE_OUTPUTDIR=<output directory>,[LOGFILE=<path to the log file>] wrapper_tredparse.sh