Remove email address

parent d7078bab
# 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/*' .`)
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### 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"
......
......@@ -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
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### 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
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### 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
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### 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
......
......@@ -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
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### 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
......
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### 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.
......
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### 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
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### 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
......
......@@ -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
......
......@@ -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
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......@@ -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
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### 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
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### 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
......
......@@ -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
......
......@@ -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
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### 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
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