UMInator.conf

/*
 * -------------------------------------------------
 *  MaestSi/UMInator Nextflow config file
 * -------------------------------------------------
 */
 
params {
    //Path to fastq files, use wildcards to select multiple samples
    fastq_files = "/path/to/samples*fastq"

    //Directory containing all scripts
    scripts_dir = "/path/to/scripts_dir"
 
    //Path to a folder where to store results
    results_dir = "/path/to/results_dir"

    //UMI design: "double" 
    //double: FW_adapter-UMI1-FW_primer-----amplicon------rc(RV_adapter-UMI2-RV_primer)
    //or      RV_adapter-UMI2-RV_primer-----amplicon------rc(FW_adapter-UMI1-FW_primer)
    
    //FW1 and RV1 are forward and reverse adapter sequences
    FW_adapter = "sequence of interest"
    RV_adapter = "sequence of interest"

    //FW2 and RV2 are forward and reverse primer sequences 
    FW_primer = "sequence of interest"
    RV_primer = "sequence of interest"
    
    //min Q value for reads filtering
    minQ = 10

    //min read length for reads filtering
    minLen = 200

    //max read length for reads filtering
    maxLen = 15000

    //Amount of bases at the beginning and end of each read to search for UMIs
    searchLen = 200

    //Cutadapt maximum allowed error rate [0, 1]
    tolCutadaptErr = 0.2

    //Min overlap between read and adapter
    minLenOvlp = 11

    //UMI length (before merging UMI1 and UMI2 in case of double UMI design)
    UMILen = 18

    //UMI structure (after merging UMI1 and UMI2, in case of double UMI design) in the form of a regex of the type: [nucl.]{cardinality}
    UMIPattern="[ATCG]{3}[CT][AG][ATCG]{3}[CT][AG][ATCG]{3}[CT][AG][ATCG]{6}[CT][AG][ATCG]{3}[CT][AG][ATCG]{3}[CT][AG][ATCG]{3}"

    //UMI clustering identity
    UMIClustID = 0.9

    //BWA aln maximum number of differences
    maxDiff = 6

    //maximum tolerated mean mapping difference between UMI and query reads
    max_NM_mean = 3

    //maximum tolerated sd of mapping difference between UMI and query reads
    max_NM_sd = 2

    //Max forks, i. e. maximum number of processes running simultaneously
    maxF=100

    //Minimum number of reads assigned to UMI for generating a consensus sequence
    min_UMI_freq=30

    //Maximum number of reads used for consensus calling
    target_reads_consensus = 200

    //Maximum number of reads used for consensus polishing
    target_reads_polishing = 200

    //fast_consensus_flag = 1 for obtaining draft consensus with VSEARCH, instead of MAFFT + EMBOSS cons
    fast_consensus_flag = 1

    //fast_polishing_flag = 1 for polishing with Racon, instead of Racon + Medaka
    fast_polishing_flag = 0

    //MAFFT plurality value: minimum fraction of aligned reads supporting a basis for including it in the preliminary consensus
    plurality=0.15

    //Set fast_alignment_flag=1 if you want to perform fast multiple sequence alignment; otherwise set fast_alignment_flag=0
    fast_alignment_flag = 1
    
    //Medaka model
    medaka_model = "r941_min_sup_g507"

    help = false

    // Flags to select which process to run
    readsFiltering = true
    candidateUMIsExtraction = true
    candidateUMIsFiltering = true
    readsUMIsAssignment = true
    QC = true
    draftConsensusCalling = true
    consensusPolishing = true
    primersTrimming = true
}

profiles {
	singularity {
	    singularity.enabled = true
	    singularity.autoMounts = false
	    //singularity.cacheDir = "/path/to/singularity/cacheDir" // if commented, work dir is going to be used
	    process {
	    cpus = 1
	    executor = 'local' // set to 'local' if you are not using a queue management system
	    queue = 'workq'
	    perJobMemLimit = true
	    queueStatInterval = '1 ms'
	    pollInterval = '1 ms'
	    container = 'maestsi/uminator:latest'
	    containerOptions = '--bind /home:/home' // adjust according to which directory you wish to make accessible to singularity

        withName:readsFiltering {
	    	cpus = { params.readsFiltering ? 1 : 1 }
	    	memory = { params.readsFiltering ? 10.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	maxRetries = 3
	    }
	    withName:candidateUMIsExtraction {
	    	cpus = { params.candidateUMIsExtraction ? 1 : 1 }
	    	memory = { params.candidateUMIsExtraction ? 10.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	maxRetries = 3
	    }
	    withName:candidateUMIsFiltering {
	    	cpus = { params.candidateUMIsFiltering ? 1 : 1 }
	    	memory = { params.candidateUMIsFiltering ? 10.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	maxRetries = 3
	    }
	    withName:readsUMIsAssignment {
	    	cpus = { params.readsUMIsAssignment ? 4 : 1 }
	    	memory = { params.readsUMIsAssignment ? 30.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	maxRetries = 3
	    }
	    withName:QC {
	    	    	cpus = { params.QC ? 4 : 1 }
	    	    	memory = { params.QC ? 30.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	    	maxRetries = 3
	   }
	    withName:draftConsensusCalling {
	    	cpus = { params.draftConsensusCalling ? 4 : 1 }
	    	memory = { params.draftConsensusCalling ? 30.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	maxRetries = 3
	    }
	    withName:consensusPolishing {
	    	cpus = { params.consensusPolishing ? 4 : 1 }
	    	memory = { params.consensusPolishing ? 20.GB + (2.GB * (task.attempt-1)) : 1.GB }
	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	maxRetries = 3
	    }
	    withName:primersTrimming {
	    	cpus = { params.primersTrimming ? 4 : 1 }
	    	memory = { params.primersTrimming ? 20.GB + (2.GB * (task.attempt-1)) : 1.GB }
	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	maxRetries = 3
	    }
	}
    }
    docker {
	    docker.enabled = true
	    docker.autoMounts = false
	    //docker.cacheDir = "/path/to/docker/cacheDir" // if commented, work dir is going to be used
	    process {
	    cpus = 1
	    executor = 'local'
            container = 'maestsi/uminator:latest'
	    containerOptions = '-v /home:/home' // adjust according to which directory you wish to make accessible to docker

        withName:readsFiltering {
	    	cpus = { params.readsFiltering ? 1 : 1 }
	    	memory = { params.readsFiltering ? 10.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	maxRetries = 3
	    }
	    withName:candidateUMIsExtraction {
	        	cpus = { params.candidateUMIsExtraction ? 1 : 1 }
	    	    	memory = { params.candidateUMIsExtraction ? 10.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	    	maxRetries = 3
	    }
	    withName:candidateUMIsFiltering {
	    	    	cpus = { params.candidateUMIsFiltering ? 1 : 1 }
	    	    	memory = { params.candidateUMIsFiltering ? 10.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	    	maxRetries = 3
	    }
	    withName:readsUMIsAssignment {
	    	    	cpus = { params.readsUMIsAssignment ? 4 : 1 }
	    	    	memory = { params.readsUMIsAssignment ? 30.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	    	maxRetries = 3
	   }
	    withName:QC {
	    	    	cpus = { params.QC ? 4 : 1 }
	    	    	memory = { params.QC ? 30.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	    	maxRetries = 3
	   }
	    withName:draftConsensusCalling {
	    	    	cpus = { params.draftConsensusCalling ? 4 : 1 }
	    	    	memory = { params.draftConsensusCalling ? 30.GB + (5.GB * (task.attempt-1)) : 1.GB }
	    	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	    	maxRetries = 3
	    }
	    withName:consensusPolishing {
	    	    	cpus = { params.consensusPolishing ? 4 : 1 }
	    	    	memory = { params.consensusPolishing ? 20.GB + (2.GB * (task.attempt-1)) : 1.GB }
	    	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	    	maxRetries = 3
	    }
	    withName:primersTrimming {
	    	cpus = { params.primersTrimming ? 4 : 1 }
	    	memory = { params.primersTrimming ? 20.GB + (2.GB * (task.attempt-1)) : 1.GB }
	    	errorStrategy = { task.exitStatus == 137 ? 'retry' : 'terminate' }
	    	maxRetries = 3
	    }
	}
    }  
}

tower {
	enabled = false
	endpoint = '-'
	accessToken = 'insert access token'
}