kkonganti@0: params {
kkonganti@0:     workflow_conceived_by = 'Kranti Konganti'
kkonganti@0:     workflow_built_by = 'Kranti Konganti'
kkonganti@0:     workflow_version = '0.5.0'
kkonganti@0:     db_mode = 'mitomine'
kkonganti@0:     db_root = '/galaxy/cfsan-centriflaken-db/nowayout'
kkonganti@0:     nowo_thresholds = 'strict'
kkonganti@0:     fastp_run = true
kkonganti@0:     fastp_failed_out = false
kkonganti@0:     fastp_merged_out = false
kkonganti@0:     fastp_overlapped_out = false
kkonganti@0:     fastp_6 = false
kkonganti@0:     fastp_reads_to_process = 0 
kkonganti@0:     fastp_fix_mgi_id = false
kkonganti@0:     fastp_A = false
kkonganti@0:     fastp_use_custom_adapters = false
kkonganti@0:     fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
kkonganti@0:         + File.separator
kkonganti@0:         + 'assets'
kkonganti@0:         + File.separator
kkonganti@0:         + 'adaptors.fa' : false)
kkonganti@0:     fastp_f = 0
kkonganti@0:     fastp_t = 0
kkonganti@0:     fastp_b = 0
kkonganti@0:     fastp_F = 0
kkonganti@0:     fastp_T = 0
kkonganti@0:     fastp_B = 0
kkonganti@0:     fastp_dedup = true
kkonganti@0:     fastp_dup_calc_accuracy = 6
kkonganti@0:     fastp_poly_g_min_len = 10
kkonganti@0:     fastp_G = true
kkonganti@0:     fastp_x = false
kkonganti@0:     fastp_poly_x_min_len = 10 
kkonganti@0:     fastp_cut_front = true
kkonganti@0:     fastp_cut_tail = false
kkonganti@0:     fastp_cut_right = true
kkonganti@0:     fastp_W = 20
kkonganti@0:     fastp_M = 30
kkonganti@0:     fastp_q = 30
kkonganti@0:     fastp_u = 40
kkonganti@0:     fastp_n = 5
kkonganti@0:     fastp_e = 0
kkonganti@0:     fastp_l = 35
kkonganti@0:     fastp_max_len = 0
kkonganti@0:     fastp_y = true
kkonganti@0:     fastp_Y = 30
kkonganti@0:     fastp_U = false
kkonganti@0:     fastp_umi_loc = false
kkonganti@0:     fastp_umi_len = false
kkonganti@0:     fastp_umi_prefix = false
kkonganti@0:     fastp_umi_skip = false
kkonganti@0:     fastp_p = true
kkonganti@0:     fastp_P = 20
kkonganti@0:     kmaalign_run = true
kkonganti@0:     kmaalign_idx = ("${params.db_root}"
kkonganti@0:         + File.separator
kkonganti@0:         + "kma"
kkonganti@0:         + File.separator
kkonganti@0:         + "${params.db_mode}")
kkonganti@0:     kmaalign_ignorequals = false
kkonganti@0:     kmaalign_int = false
kkonganti@0:     kmaalign_ef = false
kkonganti@0:     kmaalign_vcf = false
kkonganti@0:     kmaalign_sam = false
kkonganti@0:     kmaalign_nc = true
kkonganti@0:     kmaalign_na = true
kkonganti@0:     kmaalign_nf = false
kkonganti@0:     kmaalign_a = false
kkonganti@0:     kmaalign_and = true
kkonganti@0:     kmaalign_oa = false
kkonganti@0:     kmaalign_bc = false
kkonganti@0:     kmaalign_bcNano = false
kkonganti@0:     kmaalign_bcd = false
kkonganti@0:     kmaalign_bcg = false
kkonganti@0:     kmaalign_ID = (params.nowo_thresholds =~ /strict|mild/ ? 85.0 : 50.0)
kkonganti@0:     kmaalign_md = false
kkonganti@0:     kmaalign_dense = false
kkonganti@0:     kmaalign_ref_fsa = false
kkonganti@0:     kmaalign_Mt1 = false
kkonganti@0:     kmaalign_1t1 = false
kkonganti@0:     kmaalign_mrs = (params.nowo_thresholds ==~ /strict/ ? 0.99 : 0.90)
kkonganti@0:     kmaalign_mrc = (params.nowo_thresholds ==~ /strict/ ? 0.99 : 0.90)
kkonganti@0:     kmaalign_mp = (params.nowo_thresholds ==~ /strict/ ? 30 : 20)
kkonganti@0:     kmaalign_eq = (params.nowo_thresholds ==~ /strict/ ? 30 : 20)
kkonganti@0:     kmaalign_mrs = (params.nowo_thresholds ==~ /mild/ ? 0.90 : params.kmaalign_mrs)
kkonganti@0:     kmaalign_mrc = (params.nowo_thresholds ==~ /mild/ ? 0.90 : params.kmaalign_mrc)
kkonganti@0:     kmaalign_mp = (params.nowo_thresholds ==~ /mild/ ? 20 : params.kmaalign_mp)
kkonganti@0:     kmaalign_eq = (params.nowo_thresholds ==~ /mild/ ? 20 : params.kmaalign_eq)
kkonganti@0:     kmaalign_mp = (params.kmaalign_ignorequals ? 0 : params.kmaalign_mp)
kkonganti@0:     kmaalign_eq = (params.kmaalign_ignorequals ? 0 : params.kmaalign_eq)
kkonganti@0:     kmaalign_mq = false
kkonganti@0:     kmaalign_5p = false
kkonganti@0:     kmaalign_3p = false
kkonganti@0:     kmaalign_apm = false
kkonganti@0:     kmaalign_cge = false
kkonganti@0:     tuspy_gd = false
kkonganti@0:     seqkit_grep_run = true
kkonganti@0:     seqkit_grep_n = false
kkonganti@0:     seqkit_grep_s = false
kkonganti@0:     seqkit_grep_c = false
kkonganti@0:     seqkit_grep_C = false
kkonganti@0:     seqkit_grep_i = false
kkonganti@0:     seqkit_grep_v = false
kkonganti@0:     seqkit_grep_m = false
kkonganti@0:     seqkit_grep_r = false
kkonganti@0:     salmonidx_run = true
kkonganti@0:     salmonidx_k = false
kkonganti@0:     salmonidx_gencode = false
kkonganti@0:     salmonidx_features = false
kkonganti@0:     salmonidx_keepDuplicates = true
kkonganti@0:     salmonidx_keepFixedFasta = false
kkonganti@0:     salmonidx_filterSize = false
kkonganti@0:     salmonidx_sparse = false
kkonganti@0:     salmonidx_n = true
kkonganti@0:     salmonidx_decoys = false
kkonganti@0:     salmonalign_libtype = 'SF'
kkonganti@0:     ref_fna = ("${params.db_root}"
kkonganti@0:         + File.separator
kkonganti@0:         + "reference"
kkonganti@0:         + File.separator
kkonganti@0:         + "${params.db_mode}"
kkonganti@0:         + ".fna")
kkonganti@0:     sourmash_k = (params.nowo_thresholds ==~ /strict/ ? 71 : 51)
kkonganti@0:     sourmash_scale = (params.nowo_thresholds ==~ /strict/ ? 100 : 100)
kkonganti@0:     sourmashsketch_run = true
kkonganti@0:     sourmashsketch_mode = 'dna'
kkonganti@0:     sourmashsketch_file = false
kkonganti@0:     sourmashsketch_f = false
kkonganti@0:     sourmashsketch_name = false
kkonganti@0:     sourmashsketch_p = "'abund,scaled=${params.sourmash_scale},k=${params.sourmash_k}'"
kkonganti@0:     sourmashsketch_randomize = false
kkonganti@0:     sourmashgather_run = (params.sourmashsketch_run ?: false)
kkonganti@0:     sourmashgather_n = false
kkonganti@0:     sourmashgather_thr_bp = (params.nowo_thresholds ==~ /strict/ ? 100 : 100)
kkonganti@0:     sourmashgather_ignoreabn = false
kkonganti@0:     sourmashgather_prefetch = false
kkonganti@0:     sourmashgather_noprefetch = false
kkonganti@0:     sourmashgather_ani_ci = true
kkonganti@0:     sourmashgather_k = "${params.sourmash_k}"
kkonganti@0:     sourmashgather_protein = false
kkonganti@0:     sourmashgather_rna = false
kkonganti@0:     sourmashgather_nuc = false
kkonganti@0:     sourmashgather_noprotein = false
kkonganti@0:     sourmashgather_dayhoff = false
kkonganti@0:     sourmashgather_nodayhoff = false
kkonganti@0:     sourmashgather_hp = false
kkonganti@0:     sourmashgather_nohp = false
kkonganti@0:     sourmashgather_dna = true
kkonganti@0:     sourmashgather_nodna = false
kkonganti@0:     sourmashgather_scaled = false
kkonganti@0:     sourmashgather_inc_pat = false
kkonganti@0:     sourmashgather_exc_pat = false
kkonganti@0:     sfhpy_run = true
kkonganti@0:     sfhpy_fcn = 'f_match'
kkonganti@0:     sfhpy_fcv = (params.nowo_thresholds ==~ /strict/ ? "0.8" : "0.5")
kkonganti@0:     sfhpy_gt = true
kkonganti@0:     sfhpy_lt = false
kkonganti@0:     sfhpy_all = true
kkonganti@0:     lineages_csv = ("${params.db_root}"
kkonganti@0:         + File.separator
kkonganti@0:         + "taxonomy"
kkonganti@0:         + File.separator
kkonganti@0:         + "${params.db_mode}"
kkonganti@0:         + File.separator
kkonganti@0:         + "lineages.csv")
kkonganti@0:     gsalkronapy_run = true
kkonganti@0:     gsalkronapy_sf = 10000
kkonganti@0:     gsalkronapy_smres_suffix = false
kkonganti@0:     gsalkronapy_failed_suffix = false
kkonganti@0:     gsalkronapy_num_lin_cols = false
kkonganti@0:     gsalkronapy_lin_regex = false
kkonganti@0:     krona_ktIT_run = true
kkonganti@0:     krona_ktIT_n = 'all'
kkonganti@0:     krona_ktIT_q = false
kkonganti@0:     krona_ktIT_c = false
kkonganti@0:     krona_res_suffix = '.krona.tsv'
kkonganti@0:     fq_filter_by_len = 0
kkonganti@0:     fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
kkonganti@0:     fq2_suffix = '_R2_001.fastq.gz'
kkonganti@0: }