nextflow.config

conda {
    useMamba = true  // Enable Mamba
}

profiles {
    conda {
        conda.enabled          = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    mamba {
        conda.enabled          = true
        conda.useMamba         = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    docker {
        docker.enabled         = true
        docker.userEmulation   = true
        conda.enabled          = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        conda.enabled          = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
        singularity.envWhitelist = "HTTPS_PROXY,HTTP_PROXY,http_proxy,https_proxy,FTP_PROXY"
    }
    // test      { includeConfig 'conf/test.config'      }
    // test_full { includeConfig 'conf/test_full.config' }
}


// def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
// timeline {
//     enabled = true
//     file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
// }
// report {
//     enabled = true
//     file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
// }
// trace {
//     enabled = true
//     file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
// }
// dag {
//     enabled = true
//     file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
// }