nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    exscan.nf Configuration File
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Default configuration options are defined here
--------------------------------------------------------------------------------
*/

manifest {
    author                  = "Joan Lluis Pons Ramon"
    name                    = "exscan.nf"
    version                 = "0.1.0"
    description             = "An extended sequence scanner"
    homePage                = "https://github.com/jllpons/exscan"
}

params {
/*
-----------------------------
    Required Parameters
-----------------------------
**MUST** be provided as:
- Cli args:       ( `$ nextflow run main.nf --<param> <val>` )
- Yaml/JSON file: ( `$ nextflow run main -params-file params/file.yaml` )
*/
    fasta                   = null
    hmmdb                   = null

/*
-----------------------------
    Parameters with defaults
-----------------------------
Can be overwritten when provided as:
- Cli args:       ( `$ nextflow run main.nf --<param> <val>` )
- Yaml/JSON file: ( `$ nextflow run main -params-file params/file.yaml` )
*/

    sequence_type           = "dna"
    dom_ieval_filter        = "1e-03"
    min_alignment_len       = 16
    grouping_distance       = 3750 //base-pairs
    gff_intersect           = null
    keep_only_intersect     = false

    outdir                  = 'results'

/*
-----------------------------
    Optional Parameters
-----------------------------
*/
    help                    = null
    version                 = null

    // Mapping manifest so it's accessible in the main.nf script
    manifest                = manifest
}

// Load base.config by defalut for all processes
//includeConfig 'conf/base.config'


// Set bash options
process.shell = """\
bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
"""