AchabInsinguLARITY, a container to use captainAchab workflow easier !

Use a Singularity container which already has all tools to run captainAchab workflow.

First, build

singularity build <filename.simg> Singularity 

Then run

singularity run -B </PATH/TO/ANNOVAR> <filename.simg> -i workflow_inputs.json

Singularity help

singularity help <filename.simg>

-c | --conf <file.conf> : To add a conf file
-o | --option <option.json> : To add an option file
-v | --verbosity <1, 2, 3 or 4> : To set verbosity level (ERROR : 1 | WARNING : 2 | INFO [default] : 3 | DEBUG : 4)
-h | --help : Print help message in terminal and close the script (Help provided by -h concerns wrapper using)

Achabilarity is currently using a part of MobiDL which is CaptainAchab workflow.
This Singularity contains CentOS environnement and all requirements to run Captain Achab workflow (MPA, Phenolyzer, Achab) and few others (BCFTools, GATK4 ...).
Make sure you already have Annovar (and its database) to bind it. It is not include in this container. Binding of ANNOVAR and data folder (inputs) will look like:

singularity run -B /path/to/annovar/:/media -B /path/to/data/:/mnt achabilarity.simg -c /path/to/conf -i /path/to/json

The container will execute specific wrapper of cromwell (Crom-wellWrapped) which will generate the right cromwell command depending on options and arguments.

Montpellier Bioinformatique pour le Diagnostique Clinique (MoBiDiC)

CHU de Montpellier

France

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