seq_lm/nextflow.config at develop · RNABioInfo/seq_lm · GitHub

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//
// 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.

nextflow.enable.types = true

params {
    help = false
    version = false
    out_dir = "output"
    live_analysis = true
    timeline_analysis = false
    differential_expression = true
    gene_set_enrichment = true
    sample_sheet = null
    gene_sets = null
    de_lfc_cutoff = 1.0
    de_padj_cutoff = 0.05
    min_read_count = 10000
    min_replicate_sample_count = 2
    ex_name = "seq_lm"
    min_mapq = 10
    reference_genome = null
    reference_annotation = null
    ex_mk_cert = null
    ex_mk_key = null
    aws_image_prefix = null
    aws_queue = null
    disable_ping = false

    process_label = "seq_lm"
    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,wf,live_analysis'


    wf {
        chunk_qc = true
        example_cmd = [
            "--bam test_data/alignments.bam"
        ]
        container_sha = "latest"
        agent = null
    }
}

manifest {
    name            = 'rnabioinfo/seq_lm'
    author          = 'Christopher Adelmann'
    homePage        = 'https://github.com/RNABioInfo/seq_lm'
    description     = 'Live Differential Enrichment Analysis'
    mainScript      = 'main.nf'
    nextflowVersion = '>=26.04.3'
    version         = 'v0.1.5'
}

executor {
    cpus = 16
    memory = 16.GB
}

// used by default for "standard" (docker) and singularity profiles,
// other profiles may override.
process {
    withLabel:preproc {
        container = "seq_lm_preproc"
    }
    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
        }
    }


    // keep stub conda profile to prevent unknown profile warning so users get a better error
    conda {
        conda.enabled = true
    }

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

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

env {
    PYTHONNOUSERSITE = 1
}