AMPSeek/nextflow.config at main · BirolLab/AMPSeek · GitHub

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/*
 * Pipeline parameters
 */
params.data_path = "$projectDir/data"
params.output_path = "$projectDir/output"
params.threads = 30

params.download_from = null
params.output_file = null
params.time = null
params.mem = params.mem ?: '90%'  // use 90% of available memory if not specified

/*
 * Process parameters
 */
process {
    // common attributes
    withName: RUNAMPLIFY{
        container = 'quay.io/biocontainers/amplify:2.0.1--py36hdfd78af_0'
    }
    withName: RUNTAMPER{
        container = 'itsberkeucar/tamper'
    }
    withName: RUNCOLABFOLD{
        container = 'biohpc/localcolabfold:1.5'
    }
    withName: COMPILERESULTS{
        container = 'itsberkeucar/ampseek-visualization'
    }
}

/*
 * Profiles for containers and their parameters
 */
profiles{
    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
    }

    docker {
        docker.enabled = true
        docker.runOptions = "--platform=linux/amd64"
    }
}