WES.config

params {
    genome = '/hpc/diaggen/data/databases/ref_genomes/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.fasta'
    dxtracks_path = '/hpc/diaggen/software/production/Dx_tracks'

    gatk_path = '/hpc/diaggen/software/tools/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar'

    gatk_rtc_options = '--known /hpc/diaggen/data/databases/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf.gz --known /hpc/diaggen/data/databases/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz'

    gatk_ir_options = '--maxReadsInMemory 150000'

    gatk_hc_interval_list = 'Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_CREv2_SSv7_CREv4_add_100bpflank.interval_list'
    gatk_hc_interval_list_snparray = 'SNPArray/InfiniumOmni5-4v1-2.interval_list'
    gatk_hc_options = '-stand_call_conf 10 --dbsnp /hpc/diaggen/data/databases/GATK_resource_bundle/b37/dbsnp_137.b37.vcf.gz'

    gatk_snp_filter = "-filter 'QD < 2.0' -filterName SNP_LowQualityDepth -filter 'MQ < 40.0' -filterName SNP_MappingQuality -filter 'FS > 60.0' -filterName SNP_StrandBias -filter 'HaplotypeScore > 13.0' -filterName SNP_HaplotypeScoreHigh -filter 'MQRankSum < -12.5' -filterName SNP_MQRankSumLow -filter 'ReadPosRankSum < -8.0' -filterName SNP_ReadPosRankSumLow"
    gatk_snp_cluster = "--clusterSize 3 --clusterWindowSize 35"
    gatk_indel_filter = "-filter 'QD < 2.0' -filterName INDEL_LowQualityDepth -filter 'FS > 200.0' -filterName INDEL_StrandBias -filter 'ReadPosRankSum < -20.0' -filterName INDEL_ReadPosRankSumLow"

    fingerprint_target = 'fingerprint/81SNP_design.vcf'

    exoncov_path = '/hpc/diaggen/software/production/ExonCov'
    exoncov_bed = 'Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_20bpflank.bed'

    dx_resources_path = '/hpc/diaggen/software/production/Dx_resources'
    exomedepth_path = 'ExomeDepth/'
    baf_path = '/hpc/diaggen/software/production/Dx_BAF/'
    upd_path = '/hpc/diaggen/software/production/Dx_UPD/'

    clarity_epp_path = '/hpc/diaggen/software/production/clarity_epp'

    picard_bait = 'Tracks/SureSelect_CREv4_elidS34226467_Covered.list'
    picard_target = 'Tracks/ENSEMBL_UCSC_merged_collapsed_sorted_v3_20bpflank.list'

    // following resources are inside the VerifyBamID2 container (quay.io/biocontainers/verifybamid2:2.0.1--h32f71e1_2).
    contamination_path_prefix = "$params.dxtracks_path/VerifyBAMID/1000g.phase3.10k.b37.exome.vcf.gz.dat"
    contamination_sites_ud = "$params.dxtracks_path/VerifyBAMID/1000g.phase3.10k.b37.exome.vcf.gz.dat.UD"
    contamination_sites_mu = "$params.dxtracks_path/VerifyBAMID/1000g.phase3.10k.b37.exome.vcf.gz.dat.mu"
    contamination_sites_bed = "$params.dxtracks_path/VerifyBAMID/1000g.phase3.10k.b37.exome.vcf.gz.dat.bed"

    downsample_coverage = 100

    ped_folder = '/hpc/diaggen/data/ped_files/'

    gendercheck_ratio_y = 0.025
    gendercheck_mapping_qual = 20
    gendercheck_locus_y = "Y:2649520-59034050"

    cluster_options = "--mail-user $params.email --mail-type FAIL --account=diaggen"

    qc_settings_path = '/hpc/diaggen/software/production/DxNextflowWES/assets/checkqc_settings.yaml'
}

process {
    withLabel: BAF_IGV {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { (1.ms * vcf_file.size() / 110) * task.attempt }

        publishDir {
            path = "$params.outdir/baf/"
            mode = 'link'
        }
    }

    withLabel: BWA_0_7_17_Mem {
        cpus = 10
        memory = { 10.GB * task.attempt }
        time = { (1.ms * fastq.sum{it.size()} / 600) * task.attempt }
    }

    withLabel: CheckQC {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/QC/CheckQC"
            mode = 'link'
        }
    }

    withLabel: ClarityEpp_SampleUDFDx {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }
    }

    withLabel:CompareGender_Pysam {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { 5.m * task.attempt }
        publishDir {
            path = "$params.outdir/QC/GenderCheck"
            mode = 'link'
        }
    } 

    withLabel: CreateHSmetricsSummary {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/QC/Picard"
            mode = 'link'
        }
    }

    withLabel: ExomeDepth_CallCNV {
        cpus = 4
        memory = { 15.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 1400) * task.attempt }

        publishDir = [
            [path: "$params.outdir/exomedepth/UMCU", mode: 'link', pattern: 'UMCU*.vcf'],
            [path: "$params.outdir/exomedepth/HC", mode: 'link', pattern: 'HC*.vcf'],
            [path: "$params.outdir/exomedepth/logs", mode: 'link', pattern: '*.log'],
            [path: "$params.outdir/exomedepth/igv_tracks", mode: 'link', pattern: '*.igv']
        ]
    }

    withLabel: ExomeDepth_FamilyIGV {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir = [
            [path: "$params.outdir/exomedepth/", mode: 'link', pattern: '*.xml']
        ]
    }

    withLabel: ExomeDepth_GetRefset {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }
    }

    withLabel: ExomeDepth_SingleIGV {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir = [
            [path: "$params.outdir/exomedepth/", mode: 'link', pattern: '*.xml']
        ]
    }

    withLabel: ExomeDepth_Summary {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/QC/CNV"
            mode = 'link'
        }
    }

    withLabel: ExonCov_ImportBam {
        cpus = 4
        memory = { 5.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 3500) * task.attempt }
    }

    withLabel: ExonCov_SampleQC {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/QC/ExonCov"
            mode = 'link'
        }
    }

    withLabel: FASTQC_0_11_8 {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { (1.ms * fastq.sum{it.size()}/fastq.count{it} / 1000) * task.attempt }
        clusterOptions = "$params.cluster_options --gres=tmpspace:10G"

        publishDir {
            path = "$params.outdir/QC/FastQC"
            mode = 'link'
        }
    }

    withLabel: Fraction {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 1.m * task.attempt }
    }

    withLabel: GATK_3_8_1_0_gf15c1c3ef_CombineVariants {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { (1.ms * vcf_files.sum{it.size()} / 450) * task.attempt }

        publishDir {
            path = "$params.outdir"
            mode = 'link'
        }
    }

    withLabel: GATK_3_8_1_0_gf15c1c3ef_HaplotypeCaller {
        cpus = 2
        memory = { 10.GB * task.attempt }
        time = { (1.ms * bam_files.sum{it.size()} / 7000) * task.attempt }
    }

    withLabel: GATK_3_8_1_0_gf15c1c3ef_IndelRealigner {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 6000) * task.attempt }
    }

    withLabel: GATK_3_8_1_0_gf15c1c3ef_RealignerTargetCreator {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 14000) * task.attempt }
    }

    withLabel: GATK_3_8_1_0_gf15c1c3ef_SelectVariantsSample {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { (1.ms * vcf_file.size() / 750) * task.attempt }

        publishDir {
            path = "$params.outdir/single_sample_vcf"
            mode = 'link'
        }
    }

    withLabel: GATK_3_8_1_0_gf15c1c3ef_UnifiedGenotyper {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/fingerprint"
            mode = 'link'
        }
    }

    withLabel: GATK_3_8_1_0_gf15c1c3ef_VariantFiltrationSnpIndel {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { (1.ms * vcf_file.size() + 1.m) * task.attempt }
    }

    withLabel: GATK_4_2_1_0_GenotypeGVCF {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { (1.ms * gvcf_files.size() + 1.s) * task.attempt }
    }

    withLabel: GATK_4_2_1_0_HaplotypeCallerGVCF {
        cpus = 2
        memory = { 10.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 25000) * task.attempt }
    }

    withLabel: GATK_4_2_1_0_MergeVcfs {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { (1.ms * vcf_files.size() / 50000) * task.attempt }

        publishDir {
            path = "$params.outdir/baf/"
            mode = 'link'
        }
    }

    withLabel: GetStatsFromFlagstat {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/QC/Flagstat"
            mode = 'link'
        }
    }

    withLabel: Kinship {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/QC/Kinship"
            mode = 'link'
        }
    }

    withLabel: Mosdepth_0_3_3 {
        cpus = 4
        memory = { 8.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 4000) * task.attempt }
        clusterOptions = "$params.cluster_options --gres=tmpspace:10G"
    }

    withLabel: MultiQC_1_10 {
        cpus = 2
        memory = { 2.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/QC"
            mode = 'link'
        }
    }

    withLabel: ParseChildFromFullTrio {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }
    }

    withLabel: PICARD_2_22_0_IntervalListTools {
        cpus = 2
        memory = { 8.GB * task.attempt }
        time = { (1.ms * interval_list.size() / 100) * task.attempt }
        clusterOptions = "$params.cluster_options --gres=tmpspace:10G"
    }

    withLabel: PICARD_2_22_0_CollectMultipleMetrics {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 4500) * task.attempt }
        clusterOptions = "$params.cluster_options --gres=tmpspace:10G"

        publishDir {
            path = "$params.outdir/QC/Picard"
            mode = 'link'
        }
    }

    withLabel: PICARD_2_22_0_CollectHsMetrics {
        cpus = 2
        memory = { 5.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 1600) * task.attempt }
        clusterOptions = "$params.cluster_options --gres=tmpspace:10G"

        publishDir {
            path = "$params.outdir/QC/Picard"
            mode = 'link'
        }
    }

    withLabel: PICARD_2_22_0_EstimateLibraryComplexity {
        cpus = 2
        memory = { 80.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 1500) * task.attempt }
        clusterOptions = "$params.cluster_options --gres=tmpspace:100G"

        publishDir {
            path = "$params.outdir/QC/Picard"
            mode = 'link'
        }
    }

    withLabel: Sambamba_0_7_0_Flagstat {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 3000) * task.attempt }

        publishDir {
            path = "$params.outdir/QC/Flagstat"
            mode = 'link'
        }
    }

    withLabel: Sambamba_0_7_0_MarkdupMerge {
        cpus = 10
        memory = { 10.GB * task.attempt }
        time = { (1.ms * bam_files.sum{it.size()} / 8500) * task.attempt }
        clusterOptions = "$params.cluster_options --gres=tmpspace:10G"
    }

    withLabel: Sambamba_0_7_0_Merge {
        cpus = 10
        memory = { 5.GB * task.attempt }
        time = { (1.ms * bam_files.sum{it.size()} / 8000) * task.attempt }
        clusterOptions = "$params.cluster_options --gres=tmpspace:10G"

        publishDir {
            path = "$params.outdir/bam_files"
            mode = 'link'
        }
    }

    withLabel: Sambamba_0_7_0_ViewSubsample {
        cpus = 10
        memory = { 5.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 8500) * task.attempt }
        clusterOptions = "$params.cluster_options --gres=tmpspace:10G"
    }

    withLabel: Sambamba_0_7_0_ViewUnmapped {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { (1.ms * bam_file.size() / 6500) * task.attempt }
        clusterOptions = "$params.cluster_options --gres=tmpspace:10G"
    }


    withLabel: SavePedFile {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/QC/Kinship"
            mode = 'link'
        }
    }

    withLabel: UPD_IGV {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { (1.ms * vcf_files.sum{it.size()} / 200) * task.attempt }

        publishDir = [
            [path: "$params.outdir/upd/", mode: 'link', pattern: '*.igv']
        ]
    }

    withLabel: VERIFYBAMID_2_0_1_h32f71e1_2_VerifyBamID2 {
        cpus = 6
        memory = { 5.GB * task.attempt }
        time = { 20.m * task.attempt }

        publishDir {
            path = "$params.outdir/QC/VerifyBamID2"
            mode = 'link'
        }
    }

    withLabel: VersionLog {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/log"
            mode = 'link'
        }
    }

    withLabel: Workflow_Export_Params {
        cpus = 2
        memory = { 1.GB * task.attempt }
        time = { 5.m * task.attempt }

        publishDir {
            path = "$params.outdir/log"
            mode = 'link'
        }
    }
}

report {
    enabled = true
    file = "$params.outdir/log/nextflow_report.html"
    overwrite = true
}

trace {
    enabled = true
    file = "$params.outdir/log/nextflow_trace.txt"
    fields = 'task_id,hash,native_id,process,tag,name,status,exit,module,container,cpus,time,disk,memory,attempt,submit,start,complete,duration,realtime,queue,%cpu,%mem,rss,vmem,peak_rss,peak_vmem,rchar,wchar,syscr,syscw,read_bytes,write_bytes,vol_ctxt,inv_ctxt'
    overwrite = true
}

timeline {
    enabled = true
    file = "$params.outdir/log/nextflow_timeline.html"
    overwrite = true
}

profiles {

    slurm {
        process {
            executor = 'slurm'
            queue = 'cpu'
            clusterOptions = "$params.cluster_options"

            errorStrategy = 'retry'
            maxRetries = 1
        }

        singularity {
            enabled = true
            runOptions = '-B /hpc:/hpc -B $TMPDIR:$TMPDIR'
            autoMounts = true
            cacheDir = '/hpc/diaggen/software/singularity_cache'
        }

        executor {
            queueSize = 1000
            pollInterval = '1min'
            queueStatInterval = '5min'
            submitRatelimit = '10sec'
        }

       mail {
            smtp.host = 'localhost'
        }
    }

    mac {
        docker.enabled = true
        docker.runOptions = '-v /Users:/Users'
    }
}