phagomics/nextflow.config at main · Integrative-Transcriptomics/phagomics · GitHub

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#!/usr/bin/env nextflow

params.features = "./phage_data/*/*.gff"
params.proteins = "./phage_data/*/*.faa"
params.outDir = "results"
params.wsl = false
params.maxProteinLength = 1500

params.colabdb = "."        // "path/to/db/name_of_db"
params.foldseekdb = "."     // "path/to/db/name_of_db"
params.validdb = ""         // "path/to/db/name_of_db"

params.email = ""

workDir = "work"

params.help = false

cleanup = true

docker {
    enabled = true
    runOptions = "--rm"
    fixOwnership = true
}

process {
    withName: mmseqscluster {
        container = "colabfold"
    }
    withName: mmseqsclusterRefine {
        container = "colabfold"
    }
    withName: colabfold_batch {
        container = "colabfold"
    }
    withName: colabfold_batch_wsl {
        container = "colabfold"
    }

    // use this container for the rest
    container = "phagomics"
}