nextflow.config

params {
    subset_bam_to_comon_variants= true
    cell_data="None"
  // Nf core integration 
    custom_config_version      = 'master'
    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
  sample_name='hadge_process'
  outdir = "${launchDir}/results"
  mode = "rescue"
  generate_anndata = "True"
  generate_mudata = "False"
  multi_input = null  // run only one sample

  // hashing-based deconvolution
  // key input
  hto_matrix_raw = "None"
  hto_matrix_filtered = "None"
  rna_matrix_raw = "None"
  rna_matrix_filtered = "None"

  // preprocessing
  sel_method = "mean.var.plot"
  ndelim = "_"
  n_features = "2000"
  assay = "HTO"
  margin = 2
  norm_method = "CLR"
  preprocessOut = "preprocessed"
  gene_col = 2 
  
  // htodemux
  htodemux = "True"
  rna_matrix_htodemux = "filtered"
  hto_matrix_htodemux = "filtered"
  quantile_htodemux = "0.99"
  kfunc = "clara"
  nstarts = 100
  nsamples_clustering = 100
  seed = 42
  init = "None"
  objectOutHTO = "htodemux"
  assignmentOutHTO = "htodemux"
  
  // htodemux_visualization
  ridgePlot = "True"
  ridgeNCol = 3
  featureScatter = "False"
  scatterFeat1 = "None"
  scatterFeat2 = "None"
  vlnplot = "True"
  vlnFeatures = "nCount_RNA"
  vlnLog = "True"
  tsne = "True"
  tsneIdents = "Negative"
  tsneInvert = "True"
  tsneVerbose = "False"
  tsneApprox = "False"
  tsneDimMax = 2
  tsnePerplexity = 100
  heatmap = "True"
  heatmapNcells= 500
  
  // multiseq
  multiseq = "True"
  rna_matrix_multiseq = "filtered"
  hto_matrix_multiseq = "filtered"
  quantile_multi = 0.7
  autoThresh = "True"
  maxiter = 5
  qrangeFrom = 0.1
  qrangeTo = 0.9
  qrangeBy = 0.05
  verbose_multiseq = "True"
  objectOutMulti = "multiseq"
  assignmentOutMulti = "multiseq"
  
  // hashsolo
  hashsolo = "True"
  hto_matrix_hashsolo = "raw"
  rna_matrix_hashsolo = "raw"
  use_rna_data = "False"
  priors_negative = 1/3
  priors_singlet = 1/3
  priors_doublet = 1/3
  pre_existing_clusters = "None"
  number_of_noise_barcodes = "None"
  assignmentOutHashSolo = "hashsolo"
  plotOutHashSolo = "hashsolo"
  
  // hashedDrops
  hashedDrops = "True"
  hto_matrix_hashedDrops = "raw"
  lower = 100
  niters = 10000
  testAmbient = "True"
  ignore_hashedDrops = "None"
  alpha_hashedDrops = "None"
  round = "True"
  byRank = "None"
  isCellFDR = 0.01
  objectOutEmptyDrops = "emptyDroplets"
  assignmentOutEmptyDrops = "emptyDroplets"
  ambient = "True"
  minProp = 0.05
  pseudoCount = 5
  constantAmbient = "False"
  doubletNmads = 3
  doubletMin = 2
  doubletMixture = "False"
  confidentNmads = 3
  confidenMin = 2
  combinations = "None"
  objectOutHashedDrops = "hashedDrops"
  assignmentOutHashedDrops = "hashedDrops"
  runEmptyDrops = "True"
  
  // demuxem
  demuxem = "True"
  rna_matrix_demuxem = "raw"
  hto_matrix_demuxem = "raw"
  threads_demuxem = 2
  alpha_demuxem = 0.0
  alpha_noise = 1.0
  min_num_genes = 100
  min_num_umis = 100
  min_signal = 10.0
  tol = 1e-6
  random_state = 0
  generate_gender_plot = "None"
  objectOutDemuxem = "demuxem_res"
  filter_demuxem = "True"

  // gmm-demux
  gmmDemux = "True"
  hto_matrix_gmm_demux = "filtered"
  assignmentOutGmmDemux = "gmm_demux"
  hto_name_gmm = "None"
  summary = 2000
  report_gmm = "report.txt"
  mode_GMM = "tsv"
  extract = 'None' 
  threshold_gmm = 0.8
  ambiguous = 0.05

  // demuxmix
  demuxmix = "False"
  rna_matrix_demuxmix = "raw"
  hto_matrix_demuxmix = "raw"
  assignmentOutDemuxmix = "demuxmix"
  demuxmix_preprocess = "True"
  correctTails = "TRUE"
  rna_available = 'TRUE'
  model = 'naive'
  alpha_demuxmix = 0.9
  beta_demuxmix = 0.9
  tol_demuxmix = 0.00001
  maxIter_demuxmix = 1000
  k_hto = 1.5
  k_rna = 1.5

  // bff
  bff = "True"
  rna_matrix_bff = "raw"
  hto_matrix_bff = "raw"
  assignmentOutBff = "bff" 
  bff_preprocess = "True"
  methods = "combined_bff"
  methodsForConsensus = 'NULL'
  cellbarcodeWhitelist = 'NULL'
  metricsFile = 'metrics_bff.csv'
  doTSNE = "True"
  doHeatmap = "True"
  perCellSaturation = 'NULL'
  majorityConsensusThreshold = 'NULL'
  chemistry = "10xV3"
  callerDisagreementThreshold = 'NULL'
  preprocess_bff = "FALSE"
  barcodeWhitelist = 'NULL'

  // genetics-based deconvolution 
  // key input
  bam = "None"
  bai = "None"
  barcodes = "None"
  fasta = "None"
  fasta_index = "None"
  nsamples_genetic = 2
  common_variants_scSplit = "None"
  common_variants_souporcell = "None"
  common_variants_freemuxlet = "None"
  common_variants_cellsnp = "None"
  vcf_mixed = "None"
  vcf_donor = "None"
  celldata = "None"

  // demuxlet and freemuxlet
  demuxlet = "True"
  demuxlet_preprocess = "False"
  tag_group = "CB"
  tag_UMI = "UB"
  sm = "None"
  sm_list = "None"
  sam_verbose = 1000000
  vcf_verbose = 10000
  skip_umi = "False"
  cap_BQ = 40
  min_BQ = 13
  min_MQ = 20
  min_TD = 0
  excl_flag = 3844
  min_total = 0
  min_uniq = 0
  min_snp = 0
  min_umi = 0
  plp = "False"
  field = "GT"
  geno_error_offset = 0.1
  geno_error_coeff = 0.0
  r2_info = "R2"
  min_mac = 1
  min_callrate = 0.50
  alpha = "0.5" // must be string, multiple values in a single run should be comma separated
  doublet_prior = 0.5
  demuxlet_out = "demuxlet_res"

  // freemuxlet
  freemuxlet = "True"
  freemuxlet_preprocess = "False"
  init_cluster = "None"
  aux_files = "False"
  verbose = 100
  bf_thres = 5.41
  frac_init_clust = 0.5
  iter_init = 10
  keep_init_missing = "False"
  freemuxlet_out = "freemuxlet_out"

  // vireo
  vireo = "True"
  vireo_preprocess = "False"
  vireo_variant = "True"
  genoTag = "GT"
  noDoublet = "False"
  nInit = 50
  extraDonor = 0
  extraDonorMode = "distance"
  forceLearnGT = "False"
  ASEmode = "False"
  noPlot = "False"
  randSeed = "None"
  cellRange = "all"
  callAmbientRNAs = "False"
  nproc = 2
  vireo_out = "vireo_out"
 
  // souporcell
  souporcell = "True"
  souporcell_preprocess = "False"
  threads = 5
  ploidy = 2
  min_alt = 10
  min_ref = 10
  max_loci = 2048
  restarts = "None"
  use_known_genotype = "False"
  known_genotypes_sample_names = "None"
  skip_remap = "True"
  ignore = "False"
  souporcell_out = "souporcell_out"
  
  // scSplit
  scSplit = "True"
  scSplit_preprocess = "False"
  scSplit_variant = "True"
  refscSplit = "ref_filtered.csv"
  altscSplit = "alt_filtered.csv"
  subscSplit = 10
  emsscSplit = 30
  dblscSplit = "None"
  sample_geno = "False"
  scsplit_out = "scsplit_out"

  // freebayes
  stdin = "False"
  targets = "None"
  region = "None"
  samples= "None"
  populations = "None"
  cnv_map = "None"
  vcf_freebayes = "vcf_freebayes_output.vcf"
  gvcf = "False"
  gvcf_chunk = "None"
  gvcf_dont_use_chunk = "None"
  variant_input = "None"
  only_use_input_alleles = "False"
  haplotype_basis_alleles = "None"
  report_all_haplotype_alleles = "False"
  report_monomorphic  = "False"
  pvar = 0.0
  strict_vcf = "False"
  
  theta = 0.001
  pooled_discrete = "False"
  pooled_continuous = "False"
  use_reference_allele = "False"
  reference_quality = "100,60"
  no_snps = "False"
  no_indels = "True"
  no_mnps = "True"
  no_complex = "True"
  use_best_n_alleles = 0
  haplotype_length = 3
  min_repeat_size = 5
  min_repeat_entropy = 1
  no_partial_observations = "False"
  
  dont_left_align_indels = "False"
  use_duplicate_reads = "False"
  min_mapping_quality = 1
  min_base_quality = 1
  min_supporting_allele_qsum = 0
  min_supporting_mapping_qsum = 0
  mismatch_base_quality_threshold = 10
  read_mismatch_limit = "None"
  read_max_mismatch_fraction = 1.0
  read_snp_limit = "None"
  read_indel_limit = "None"
  standard_filters = "False"
  min_alternate_fraction = 0.05
  min_alternate_count = 2
  min_alternate_qsum = 0
  min_alternate_total = 1
  min_coverage = 0
  max_coverage = "None"
  no_population_priors = "False"
  hwe_priors_off = "False"
  binomial_obs_priors_off = "False"
  allele_balance_priors_off = "False"
  observation_bias = "None"
  base_quality_cap = "None"
  prob_contamination = 0.000000001
  legacy_gls= "False"
  contamination_estimates = "None"
  report_genotype_likelihood_max = "False"
  genotyping_max_iterations = 1000
  genotyping_max_banddepth = 6
  posterior_integration_limits = "1,3"
  exclude_unobserved_genotypes = "False"
  genotype_variant_threshold = "None"
  use_mapping_quality = "False"
  harmonic_indel_quality = "False"
  read_dependence_factor = 0.9
  genotype_qualities= "False"
  debug = "False"
  dd = "False"
  // cellsnp 
  targetsVCF = "None"
  sampleList  = "None"
  sampleIDs = "None"
  genotype_cellSNP = "True"
  gzip_cellSNP = "True"
  printSkipSNPs = "False"
  nproc_cellSNP = 2
  refseq_cellSNP = "None"
  chrom = "None"
  cellTAG = "CB"
  UMItag = "Auto"
  minCOUNT = 20
  minMAF = 0.1
  doubletGL = "False"
  inclFLAG = "None"
  exclFLAG = "None"
  minLEN = 30
  minMAPQ = 20
  maxDEPTH = 0
  countORPHAN = "False"
  cellsnp_out = "cellSNP_out"
  
  // donor matching
  match_donor = "True"
  demultiplexing_result = "None"
  match_donor_method1 = "None"
  match_donor_method2 = "None"
  findVariants = "False"
  variant_count = 10
  variant_pct = 0.9
  vireo_parent_dir = "None"
}

profiles {
    standard {
        process {
            executor = 'local'
            withLabel: big_mem {
                cpus = 4
                memory = 150.GB
            }
            withLabel: small_mem {
                cpus = 2
                memory = 100.GB
            }
        }
        
    }
    cluster {
        process {
            executor = 'slurm'
            maxRetries = 3 
            // queue = ...
            // clusterOptions =  ...
	        withLabel: big_mem {
                cpus = 16
                memory = {30.GB * task.attempt}
                time =24.h
            }
            withLabel: small_mem {
                cpus = 6
                memory = {20.GB * task.attempt}
                time =24.h
            }


            withName: subset_bam_to_comon_variants{
                cpus = 2
                memory = {20.GB * task.attempt}
            }            

            withName: summary{
                cpus = 1
                memory = {10.GB * task.attempt}
            }

            withName: matchDonor{
                cpus = {2 * task.attempt}
                memory = {10.GB * task.attempt }
            }

            withName:souporcell{
                time = 48.h
            }
        }
    }
    conda {
        conda.enabled          = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    docker {
        docker.enabled         = true
        docker.registry        = 'quay.io'
        docker.userEmulation   = true
        conda.enabled          = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    arm {
        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
    }
    singularity {
        singularity.enabled    = true
        singularity.runOptions = "--bind $PWD"
        singularity.cacheDir   = "$PWD"
        conda.enabled          = false
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false
    }
    test { 
        includeConfig 'test.config'
    }
    conda_singularity { 
        singularity.enabled    = true
        singularity.runOptions = "--bind $PWD"
        singularity.cacheDir   = "$PWD"
        conda.enabled          = true
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
        apptainer.enabled      = false   
    }
}

process {
    echo = true
    debug = true
    maxRetries    = 3
    maxErrors     = '-1'
    errorStrategy = 'retry'
}


try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")

}