MetaDiversity-Pipeline/cluster.config at main · JackSherry6/MetaDiversity-Pipeline · GitHub

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params {
    // Reads and references
    samplesheet = "$projectDir/samplesheet.csv"
    classifier = "$projectDir/bin/silva-138.2-ssu-nr99-341f-806r-classifier.qza"
    metadata = "$projectDir/metadata.tsv"
    sampling_depth = 60000  //Set these accordingly
    rarefaction_depth = 5000  //Set these accordingly

    // Directories
    outdir = "$projectDir/results/"
    refdir = "$projectDir/refs/"
}

profiles {
    conda {
        conda.enabled = true
    }

    singularity {
        singularity.enabled = true
        singularity.autoMounts = true
        singularity.cacheDir = '/projectnb/bf528/students/jgsherry/singularity_cache'
    }

    cluster {
        process {
            executor = 'sge'
            clusterOptions = '-P bf528'
            penv = 'omp'

            // Module setup for QIIME2 processes
            withName: 'QIIME2_.*' {
                beforeScript = '''
                    set +u
                    if [ -f /share/pkg.8/qiime2/2025.4.0/install-amplicon/etc/profile.d/conda.sh ]; then
                        source /share/pkg.8/qiime2/2025.4.0/install-amplicon/etc/profile.d/conda.sh
                        conda activate /share/pkg.8/qiime2/2025.4.0/install-amplicon
                    else
                        export PATH=/share/pkg.8/qiime2/2025.4.0/install-amplicon/bin:$PATH
                        export CONDA_PREFIX=/share/pkg.8/qiime2/2025.4.0/install-amplicon
                        export PYTHONPATH=/share/pkg.8/qiime2/2025.4.0/install-amplicon/lib/python3.10/site-packages:$PYTHONPATH
                    fi
                '''.stripIndent()
            }

            withLabel: process_single {
                cpus = 1
            }

            withLabel: process_low {
                cpus = 4
            }

            withLabel: process_medium {
                cpus = 8
            }

            withLabel: process_high {
                cpus = 16
            }
        }
    }

    local {
        process.executor = 'local'
    }
}

executor {
    $sge {
        queueSize = 8
    }
    $local {
        cpus = 1
    }
}

resume = true