README.md

CBCRG lab nextflow configs

Repository to share nextflow configurations files used by the cbcrg-lab.

How to use a config file

Including the configuration under a profile on the nextflow.config

Pick any of the configuration files (e.g. crg_cbcrg.config), move it to the conf folder of your Nextflow pipeline (or any other folder you decide to use to place the configuration files) and include it using the code below on your nextflow.config

profiles {
    crg {
        // Load the config file
        includeConfig 'conf/config_foo.config'
    }
}

The profiles of the nextflow.config file become available and can be used specifying the -profile option of Nextflow (see here. Now you can use the crg profile with the command below:

nextflow run <your_script> -profile crg

BOVREG project reporting

Note, that the configuration file also includes a nested profile corresponding to the BovReg project, see here. In the case you want to report your computations to the project you can just use the command below:

nextflow run <your_script> -profile crg,bovreg

Note, that you can only report computations perform on the long and short shared queues (long-sl7 and short-sl7 respectively) to the BovReg project. If you computation is urgent keep in mind that these queues might have longing wating times!!!

Use directly the configuration file

Place the configuration file e.g. crg_cbcrg.config on the folder you decide.

Run your pipeline using the -c option:

nextflow run <your_script> -c /path/to/config/crg_cbcrg.config

BOVREG project reporting

On this case you just need to set the bovreg profile since all the other settings are directly load from the configuration file:

nextflow run <your_script> -c /path/to/config/crg_cbcrg.config -profile bovreg