wf-transcriptomes-v202/nextflow.config

//
// Notes to End Users.
//
// The workflow should run without editing this configuration file,
// however there may be instances in which you wish to edit this
// file for compute performance or other reasons. Please see:
//
//   https://nextflow.io/docs/latest/config.html#configuration
//
// for further help editing this file.


params {
    help = false
    fastq = null
    ref_genome = null
    ref_annotation = null
    // Process cDNA reads using pychopper, turn off for direct RNA:
    use_pychopper = true
    threads = 4

    out_dir = null
    sample = null
    sample_sheet = null
    sanitize_fastq = false
    wfversion = "v0.0.1"
    aws_image_prefix = null
    aws_queue = null
    report_name = "report"

    monochrome_logs = false
    validate_params = true
    show_hidden_params = false
    schema_ignore_params = 'show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wfversion'


    // Options passed to pychopper:
    pychopper_opts = ""

    // Extra option passed to minimap2 when generating index
    minimap_index_opts = "-k14"

    // Extra options passed to minimap2
    minimap2_opts = "-uf"
    // Add this for SIRV data:
    // "--splice-flank=no"

    // Minmum mapping quality
    minimum_mapping_quality = 40

    // Internal priming filter context size:
    poly_context = 24

    // Maximum allowed poly(A) length in the genome near the 3' end of mapping: 
    max_poly_run = 8

    // Minimium number of reads in BAM bundles:
    bundle_min_reads = 50000

    // Options passed to stringtie:
    stringtie_opts = " --conservative "

    // Options passed to gffcompare:
    gffcompare_opts = " -R "

    // Plot gffcompare results:
    plot_gffcmp_stats = true

    disable_ping = false
}

manifest {
    name            = 'epi2me-labs/wf-isoforms'
    author          = 'Oxford Nanopore Technologies'
    homePage        = 'https://github.com/epi2me-labs/wf-isoforms'
    description     = 'RNA/cDNA isoform analysis workflow'
    mainScript      = 'main.nf'
    nextflowVersion = '>=20.10.0'
    //version       = 'v0.0.7'  // TODO: do switch to this?
}

executor {
    $local {
        cpus = 4
        memory = "8 GB"
    }
}

// used by default for "standard" (docker) and singularity profiles,
// other profiles may override.
process {
    withLabel:isoforms {
        container = "ontresearch/wf-isoforms:${params.wfversion}"
    }
    shell = ['/bin/bash', '-euo', 'pipefail']
}


profiles {
    // the "standard" profile is used implicitely by nextflow
    // if no other profile is given on the CLI
    standard {
        docker {
            enabled = true
            // this ensures container is run as host user and group, but
            //    also adds host user to the within-container group
            runOptions = "--user \$(id -u):\$(id -g) --group-add 100"
        }
    }

    // using singularity instead of docker
    singularity {
        singularity {
            enabled = true
            autoMounts = true
        }
    }


    // profile using conda environments
    conda {
        docker.enabled = false
        process {
            withLabel:isoforms {
                conda = "${projectDir}/environment.yaml"
            }
            shell = ['/bin/bash', '-euo', 'pipefail']
        }
        conda {
             cacheDir = ""
             useMamba = true
        }
    }

    // Using AWS batch.
    // May need to set aws.region and aws.batch.cliPath
    awsbatch {
        process {
            executor = 'awsbatch'
            queue = "${params.aws_queue}"
            memory = '8G'
            withLabel:isoforms {
                container = "${params.aws_image_prefix}-wf-isoforms:${params.wfversion}"
            }
            shell = ['/bin/bash', '-euo', 'pipefail']
        }
    }

    // local profile for simplified development testing
    local {
        process.executor = 'local'
    }
}


timeline {
  enabled = true
  file = "${params.out_dir}/execution/timeline.html"
}
report {
  enabled = true
  file = "${params.out_dir}/execution/report.html"
}
trace {
  enabled = true
  file = "${params.out_dir}/execution/trace.txt"
}
dag {
  enabled = true
  file = "${params.out_dir}/execution/pipeline.svg"
}