nextflow.config

/*
vim: syntax=groovy
-*- mode: groovy;-*-
 * -------------------------------------------------
 *  NF-CAGEseq Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 * Cluster-specific config options should be saved
 * in the conf folder and imported under a profile
 * name here.
 */

// Variable to specify the docker / singularity image tag to use
// Picks up on use of -r 1.3 in nextflow command
wf_container = { "kevinmenden/tf-activity:latest" }

// Global default params, used in configs
params {

    // Pipeline version
    version = '0.1.0dev'
    outdir = './results'
    igenomes_base = "./iGenomes"
    clusterOptions = false
    // Docker container
    container = 'kevinmenden/tf-activity:latest'

}

profiles {

    standard
    {
        includeConfig 'conf/base.config'
    }
    docker
    {
        includeConfig 'conf/base.config'
        includeConfig 'conf/docker.config'
    }
    human
    {
        includeConfig 'conf/base.config'
        includeConfig 'conf/docker.config'
        includeConfig 'conf/human.config'
    }

}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

timeline {
  enabled = true
  file = "${params.outdir}/pipeline_info/NF-CAGEseq_timeline.html"
}
report {
  enabled = true
  file = "${params.outdir}/pipeline_info/NF-CAGEseq_report.html"
}
trace {
  enabled = true
  file = "${params.outdir}/pipeline_info/NF-CAGEseq_trace.txt"
}
dag {
  enabled = true
  file = "${params.outdir}/pipeline_info/NF-CAGEseq_dag.html"
}


manifest {
    homePage = 'https://github.com/KevinMenden/tf-activity'
    description = 'Pipeline for active TF identification from CAGE-seq peaks'
    mainScript = 'main.nf'
}