--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/workflows/conf/nowayout.config	Mon Mar 31 14:50:40 2025 -0400
@@ -0,0 +1,180 @@
+params {
+    workflow_conceived_by = 'Kranti Konganti'
+    workflow_built_by = 'Kranti Konganti'
+    workflow_version = '0.5.0'
+    db_mode = 'mitomine'
+    db_root = '/galaxy/cfsan-centriflaken-db/nowayout'
+    nowo_thresholds = 'strict'
+    fastp_run = true
+    fastp_failed_out = false
+    fastp_merged_out = false
+    fastp_overlapped_out = false
+    fastp_6 = false
+    fastp_reads_to_process = 0 
+    fastp_fix_mgi_id = false
+    fastp_A = false
+    fastp_use_custom_adapters = false
+    fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
+        + File.separator
+        + 'assets'
+        + File.separator
+        + 'adaptors.fa' : false)
+    fastp_f = 0
+    fastp_t = 0
+    fastp_b = 0
+    fastp_F = 0
+    fastp_T = 0
+    fastp_B = 0
+    fastp_dedup = true
+    fastp_dup_calc_accuracy = 6
+    fastp_poly_g_min_len = 10
+    fastp_G = true
+    fastp_x = false
+    fastp_poly_x_min_len = 10 
+    fastp_cut_front = true
+    fastp_cut_tail = false
+    fastp_cut_right = true
+    fastp_W = 20
+    fastp_M = 30
+    fastp_q = 30
+    fastp_u = 40
+    fastp_n = 5
+    fastp_e = 0
+    fastp_l = 35
+    fastp_max_len = 0
+    fastp_y = true
+    fastp_Y = 30
+    fastp_U = false
+    fastp_umi_loc = false
+    fastp_umi_len = false
+    fastp_umi_prefix = false
+    fastp_umi_skip = false
+    fastp_p = true
+    fastp_P = 20
+    kmaalign_run = true
+    kmaalign_idx = ("${params.db_root}"
+        + File.separator
+        + "kma"
+        + File.separator
+        + "${params.db_mode}")
+    kmaalign_ignorequals = false
+    kmaalign_int = false
+    kmaalign_ef = false
+    kmaalign_vcf = false
+    kmaalign_sam = false
+    kmaalign_nc = true
+    kmaalign_na = true
+    kmaalign_nf = false
+    kmaalign_a = false
+    kmaalign_and = true
+    kmaalign_oa = false
+    kmaalign_bc = false
+    kmaalign_bcNano = false
+    kmaalign_bcd = false
+    kmaalign_bcg = false
+    kmaalign_ID = (params.nowo_thresholds =~ /strict|mild/ ? 85.0 : 50.0)
+    kmaalign_md = false
+    kmaalign_dense = false
+    kmaalign_ref_fsa = false
+    kmaalign_Mt1 = false
+    kmaalign_1t1 = false
+    kmaalign_mrs = (params.nowo_thresholds ==~ /strict/ ? 0.99 : 0.90)
+    kmaalign_mrc = (params.nowo_thresholds ==~ /strict/ ? 0.99 : 0.90)
+    kmaalign_mp = (params.nowo_thresholds ==~ /strict/ ? 30 : 20)
+    kmaalign_eq = (params.nowo_thresholds ==~ /strict/ ? 30 : 20)
+    kmaalign_mrs = (params.nowo_thresholds ==~ /mild/ ? 0.90 : params.kmaalign_mrs)
+    kmaalign_mrc = (params.nowo_thresholds ==~ /mild/ ? 0.90 : params.kmaalign_mrc)
+    kmaalign_mp = (params.nowo_thresholds ==~ /mild/ ? 20 : params.kmaalign_mp)
+    kmaalign_eq = (params.nowo_thresholds ==~ /mild/ ? 20 : params.kmaalign_eq)
+    kmaalign_mp = (params.kmaalign_ignorequals ? 0 : params.kmaalign_mp)
+    kmaalign_eq = (params.kmaalign_ignorequals ? 0 : params.kmaalign_eq)
+    kmaalign_mq = false
+    kmaalign_5p = false
+    kmaalign_3p = false
+    kmaalign_apm = false
+    kmaalign_cge = false
+    tuspy_gd = false
+    seqkit_grep_run = true
+    seqkit_grep_n = false
+    seqkit_grep_s = false
+    seqkit_grep_c = false
+    seqkit_grep_C = false
+    seqkit_grep_i = false
+    seqkit_grep_v = false
+    seqkit_grep_m = false
+    seqkit_grep_r = false
+    salmonidx_run = true
+    salmonidx_k = false
+    salmonidx_gencode = false
+    salmonidx_features = false
+    salmonidx_keepDuplicates = true
+    salmonidx_keepFixedFasta = false
+    salmonidx_filterSize = false
+    salmonidx_sparse = false
+    salmonidx_n = true
+    salmonidx_decoys = false
+    salmonalign_libtype = 'SF'
+    ref_fna = ("${params.db_root}"
+        + File.separator
+        + "reference"
+        + File.separator
+        + "${params.db_mode}"
+        + ".fna")
+    sourmash_k = (params.nowo_thresholds ==~ /strict/ ? 71 : 51)
+    sourmash_scale = (params.nowo_thresholds ==~ /strict/ ? 100 : 100)
+    sourmashsketch_run = true
+    sourmashsketch_mode = 'dna'
+    sourmashsketch_file = false
+    sourmashsketch_f = false
+    sourmashsketch_name = false
+    sourmashsketch_p = "'abund,scaled=${params.sourmash_scale},k=${params.sourmash_k}'"
+    sourmashsketch_randomize = false
+    sourmashgather_run = (params.sourmashsketch_run ?: false)
+    sourmashgather_n = false
+    sourmashgather_thr_bp = (params.nowo_thresholds ==~ /strict/ ? 100 : 100)
+    sourmashgather_ignoreabn = false
+    sourmashgather_prefetch = false
+    sourmashgather_noprefetch = false
+    sourmashgather_ani_ci = true
+    sourmashgather_k = "${params.sourmash_k}"
+    sourmashgather_protein = false
+    sourmashgather_rna = false
+    sourmashgather_nuc = false
+    sourmashgather_noprotein = false
+    sourmashgather_dayhoff = false
+    sourmashgather_nodayhoff = false
+    sourmashgather_hp = false
+    sourmashgather_nohp = false
+    sourmashgather_dna = true
+    sourmashgather_nodna = false
+    sourmashgather_scaled = false
+    sourmashgather_inc_pat = false
+    sourmashgather_exc_pat = false
+    sfhpy_run = true
+    sfhpy_fcn = 'f_match'
+    sfhpy_fcv = (params.nowo_thresholds ==~ /strict/ ? "0.8" : "0.5")
+    sfhpy_gt = true
+    sfhpy_lt = false
+    sfhpy_all = true
+    lineages_csv = ("${params.db_root}"
+        + File.separator
+        + "taxonomy"
+        + File.separator
+        + "${params.db_mode}"
+        + File.separator
+        + "lineages.csv")
+    gsalkronapy_run = true
+    gsalkronapy_sf = 10000
+    gsalkronapy_smres_suffix = false
+    gsalkronapy_failed_suffix = false
+    gsalkronapy_num_lin_cols = false
+    gsalkronapy_lin_regex = false
+    krona_ktIT_run = true
+    krona_ktIT_n = 'all'
+    krona_ktIT_q = false
+    krona_ktIT_c = false
+    krona_res_suffix = '.krona.tsv'
+    fq_filter_by_len = 0
+    fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
+    fq2_suffix = '_R2_001.fastq.gz'
+}
\ No newline at end of file