|Description||Hands On Lab Exercises for TOGGLe|
|Related-course materials||TOGGLe introduction|
|Authors||Sébastien RAVEL (email@example.com)
Christine TRANCHANT (firstname.lastname@example.org)
|Last Modified Date||16/04/2019|
Creating your own workflow :
Practice 1 consists of using base one pre-defined configuration file to build own workflow to use with TOGGLe.
The SNPdiscoveryPaired.config.txt file is an example of how to customize your pipeline.
The order of a pipeline is provided with key $order, base on the file, build new config file to run only from mapping to SNP calling.
All input data:
- Input data : /data2/formation/TPsnpSV/fastqDir/
- Reference : /data2/formation/TPsnpSV/reference.fasta
- Config file: /data2/formation/TPsnpSV/configFiles/SNPdiscoveryPaired.config.txt
- Create a “formationX” directory in your account
- Make à copy for reference and input data into “formationX” directory (scp).
- Add the configuration file used by TOGGLe and change SGE key as below
Connect to account and prepare datas:
- Connect to the cluster:
- Launch a QRSH command:
- Transfer the data from nas using SCP:
- Load TOGGLe tools:
Launching an analysis
Use only one script to run all pipeline: toggleGenerator.pl script usage
|Required named arguments:|
|-d / –directory DIR:||a folder with raw data to be treated (FASTQ, FASTQ.GZ, SAM, BAM, VCF)|
|-c / –config FILE:||generally it is the software.config.txt file but it can be any text file structured as shown below.|
|-o / –outputdir DIR:||the current version of TOGGLE will not modify the initial data folder but will create an output directory with all analyses in.|
|Optional named arguments:|
|-r / –reference FILE:||the reference FASTA file to be used. (1)|
|-g / -gff FILE:||the GFF file to be used for some tools.|
|-k / –keyfile FILE:||the keyfile use for demultiplexing step.|
|-nocheck / –nocheckFastq:||by default toggle checks if fastq format is correct in every file. This option allows to skip this step.|
|-report / –report:||generate pdf report (more info)|
|-h / –help:||show help message and exit|
(1): If no database index exists, it will be automatically created if it is necessary. If the index already exists, they will not be re-created UNLESS the pipeline order (see below) expressively requests it (updating the index e.g.)
All the the paths (files and folders) can be provided as absolute (/home/mylogin/data/myRef.fasta) or relative (../data/myRef.fasta).
Example of a command to run TOGGLe :
- Related courses : TOGGLe