nextflow.config

/**
 * =============================================================================
 *                       Pynome-nf Configuration File
 * =============================================================================
 * This file provides the configuration settings for the Pynome-nf workflow.
 * It is designed to provide workflow parameter settings in this file. These
 * are the settings needed for proper execution of the workflow processes. More
 * advanced configuration settings are avilable via included configuration
 * files that are found in the ./config directory.
 *
 * Most users will only need to edit the settings in this file and
 * the appropriate profile settings file if executing Pynome other than
 * standalone.  Pynome provides default configuration files for
 * Standalone Docker, Standalone Singularity, PBS cluster, SLURM cluster and
 * a Kubernetes cluster.
 *
 */

// These lines include the settings from the version and manifest configuration
// files. To ensure reproducibilty of the workflow, these configuration files
// should not be edited.
includeConfig "VERSION"
includeConfig "config/manifest.config"

params {
    input {
        // set to 'all' to find all available species.
        species = 'cartosa'
    }
    output {
        // The full path on the system where genomes should be housed.
        pynome_data_dir = '/local/genomes'
    }
    execution {
        queue_size = 2
    }
}

// GENERAL SETTINGS
// ----------------
// The following includes default configurations that support reporting,
// containers, and default settings for execution of processes. If you need to
// override any of the settings in these files pleace do not edit the files
// themselves, but instead reenter the settings below to override them.
includeConfig "config/reports.config"
includeConfig "config/singularity.config"
includeConfig "config/docker.config"
includeConfig "config/process.config"

// PROFILE SETTINGS
// ----------------
// You will be executing AnnoTater on one ore more platforms. The following
// provides default configruation settings for multiple types of platform
// profiles.  You will want to override these settings for the platforms on
// which you are working.  Do not edit the config files listed here but instead
// you can override the settings in the space below.
includeConfig "config/profiles/docker.config"
includeConfig "config/profiles/singularity.config"
includeConfig "config/profiles/standard.config"
includeConfig "config/profiles/travis.config"
includeConfig "config/profiles/testing.config"
includeConfig "config/profiles/k8s.config"
includeConfig "config/profiles/slurm.config"
includeConfig "config/profiles/pbs.config"

// Overide default settings in this space