target-asm/nextflow.config at main · Yixuan39/target-asm · GitHub

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params {
    reads = null
    gx_db = null
    tax_id = null
    target_bases = null
    rasusa_seed = 0
    outdir = '.'
    threads = 24
    help = false
    hifiasm_option = '-l 2'
    keep_intermediates = false
    quality_library = null
    quality_lineage = ''
    fcs_gx_memory = '512 GB'
}


// Container definitions for Biocontainers
process {
    withName: metamdbg_assemble {
        container = 'quay.io/biocontainers/metamdbg:1.2--h077b44d_0'
    }
    withName: minimap2_run {
        container = 'quay.io/biocontainers/minimap2:2.28--h577a1d6_4'
    }
    withName: samtools_filter {
        container = 'quay.io/biocontainers/samtools:1.22.1--h96c455f_0'
    }
    withName: rasusa_subset {
        container = 'quay.io/biocontainers/rasusa:2.2.2--hc1c3326_0'
    }
    withName: hifiasm_run {
        container = 'quay.io/biocontainers/hifiasm:0.25.0--h5ca1c30_0'
    }
    withName: gfatools_convert {
        container = 'quay.io/biocontainers/gfatools:0.5.5--h577a1d6_0'
    }

    withName: compleasm_run {
        container = 'quay.io/biocontainers/compleasm:0.2.7--pyh7e72e81_1'
    }
    withName: quast_run {
        container = 'quay.io/biocontainers/quast:5.3.0--py313pl5321h5ca1c30_2'
    }
    withName: 'deliver_final_clean' {
        container = 'ubuntu:22.04'
    }
    withName: 'merge_quality_reports' {
        container = 'ubuntu:22.04'
    }
    withName: fcs_gx_initial_clean {
        memory = params.fcs_gx_memory
    }
    withName: fcs_gx_final_clean {
        memory = params.fcs_gx_memory
    }
}

profiles {
    standard {
        process {
            executor = 'local'
        }
    }
    slurm {
        process {
            executor = 'slurm'
        }
    }

    docker {
        docker.enabled = true
    }
    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
    }
    apptainer {
        apptainer.enabled = true
        apptainer.autoMounts = true
    }
}