Mercurial > repos > kkonganti > hfp_nowayout

comparison 0.5.0/workflows/conf/nowayout.config @ 0:97cd2f532efe

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planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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-1:000000000000 0:97cd2f532efe
1 params {
2 workflow_conceived_by = 'Kranti Konganti'
3 workflow_built_by = 'Kranti Konganti'
4 workflow_version = '0.5.0'
5 db_mode = 'mitomine'
6 db_root = '/galaxy/cfsan-centriflaken-db/nowayout'
7 nowo_thresholds = 'strict'
8 fastp_run = true
9 fastp_failed_out = false
10 fastp_merged_out = false
11 fastp_overlapped_out = false
12 fastp_6 = false
13 fastp_reads_to_process = 0
14 fastp_fix_mgi_id = false
15 fastp_A = false
16 fastp_use_custom_adapters = false
17 fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
18 + File.separator
19 + 'assets'
20 + File.separator
21 + 'adaptors.fa' : false)
22 fastp_f = 0
23 fastp_t = 0
24 fastp_b = 0
25 fastp_F = 0
26 fastp_T = 0
27 fastp_B = 0
28 fastp_dedup = true
29 fastp_dup_calc_accuracy = 6
30 fastp_poly_g_min_len = 10
31 fastp_G = true
32 fastp_x = false
33 fastp_poly_x_min_len = 10
34 fastp_cut_front = true
35 fastp_cut_tail = false
36 fastp_cut_right = true
37 fastp_W = 20
38 fastp_M = 30
39 fastp_q = 30
40 fastp_u = 40
41 fastp_n = 5
42 fastp_e = 0
43 fastp_l = 35
44 fastp_max_len = 0
45 fastp_y = true
46 fastp_Y = 30
47 fastp_U = false
48 fastp_umi_loc = false
49 fastp_umi_len = false
50 fastp_umi_prefix = false
51 fastp_umi_skip = false
52 fastp_p = true
53 fastp_P = 20
54 kmaalign_run = true
55 kmaalign_idx = ("${params.db_root}"
56 + File.separator
57 + "kma"
58 + File.separator
59 + "${params.db_mode}")
60 kmaalign_ignorequals = false
61 kmaalign_int = false
62 kmaalign_ef = false
63 kmaalign_vcf = false
64 kmaalign_sam = false
65 kmaalign_nc = true
66 kmaalign_na = true
67 kmaalign_nf = false
68 kmaalign_a = false
69 kmaalign_and = true
70 kmaalign_oa = false
71 kmaalign_bc = false
72 kmaalign_bcNano = false
73 kmaalign_bcd = false
74 kmaalign_bcg = false
75 kmaalign_ID = (params.nowo_thresholds =~ /strict|mild/ ? 85.0 : 50.0)
76 kmaalign_md = false
77 kmaalign_dense = false
78 kmaalign_ref_fsa = false
79 kmaalign_Mt1 = false
80 kmaalign_1t1 = false
81 kmaalign_mrs = (params.nowo_thresholds ==~ /strict/ ? 0.99 : 0.90)
82 kmaalign_mrc = (params.nowo_thresholds ==~ /strict/ ? 0.99 : 0.90)
83 kmaalign_mp = (params.nowo_thresholds ==~ /strict/ ? 30 : 20)
84 kmaalign_eq = (params.nowo_thresholds ==~ /strict/ ? 30 : 20)
85 kmaalign_mrs = (params.nowo_thresholds ==~ /mild/ ? 0.90 : params.kmaalign_mrs)
86 kmaalign_mrc = (params.nowo_thresholds ==~ /mild/ ? 0.90 : params.kmaalign_mrc)
87 kmaalign_mp = (params.nowo_thresholds ==~ /mild/ ? 20 : params.kmaalign_mp)
88 kmaalign_eq = (params.nowo_thresholds ==~ /mild/ ? 20 : params.kmaalign_eq)
89 kmaalign_mp = (params.kmaalign_ignorequals ? 0 : params.kmaalign_mp)
90 kmaalign_eq = (params.kmaalign_ignorequals ? 0 : params.kmaalign_eq)
91 kmaalign_mq = false
92 kmaalign_5p = false
93 kmaalign_3p = false
94 kmaalign_apm = false
95 kmaalign_cge = false
96 tuspy_gd = false
97 seqkit_grep_run = true
98 seqkit_grep_n = false
99 seqkit_grep_s = false
100 seqkit_grep_c = false
101 seqkit_grep_C = false
102 seqkit_grep_i = false
103 seqkit_grep_v = false
104 seqkit_grep_m = false
105 seqkit_grep_r = false
106 salmonidx_run = true
107 salmonidx_k = false
108 salmonidx_gencode = false
109 salmonidx_features = false
110 salmonidx_keepDuplicates = true
111 salmonidx_keepFixedFasta = false
112 salmonidx_filterSize = false
113 salmonidx_sparse = false
114 salmonidx_n = true
115 salmonidx_decoys = false
116 salmonalign_libtype = 'SF'
117 ref_fna = ("${params.db_root}"
118 + File.separator
119 + "reference"
120 + File.separator
121 + "${params.db_mode}"
122 + ".fna")
123 sourmash_k = (params.nowo_thresholds ==~ /strict/ ? 71 : 51)
124 sourmash_scale = (params.nowo_thresholds ==~ /strict/ ? 100 : 100)
125 sourmashsketch_run = true
126 sourmashsketch_mode = 'dna'
127 sourmashsketch_file = false
128 sourmashsketch_f = false
129 sourmashsketch_name = false
130 sourmashsketch_p = "'abund,scaled=${params.sourmash_scale},k=${params.sourmash_k}'"
131 sourmashsketch_randomize = false
132 sourmashgather_run = (params.sourmashsketch_run ?: false)
133 sourmashgather_n = false
134 sourmashgather_thr_bp = (params.nowo_thresholds ==~ /strict/ ? 100 : 100)
135 sourmashgather_ignoreabn = false
136 sourmashgather_prefetch = false
137 sourmashgather_noprefetch = false
138 sourmashgather_ani_ci = true
139 sourmashgather_k = "${params.sourmash_k}"
140 sourmashgather_protein = false
141 sourmashgather_rna = false
142 sourmashgather_nuc = false
143 sourmashgather_noprotein = false
144 sourmashgather_dayhoff = false
145 sourmashgather_nodayhoff = false
146 sourmashgather_hp = false
147 sourmashgather_nohp = false
148 sourmashgather_dna = true
149 sourmashgather_nodna = false
150 sourmashgather_scaled = false
151 sourmashgather_inc_pat = false
152 sourmashgather_exc_pat = false
153 sfhpy_run = true
154 sfhpy_fcn = 'f_match'
155 sfhpy_fcv = (params.nowo_thresholds ==~ /strict/ ? "0.8" : "0.5")
156 sfhpy_gt = true
157 sfhpy_lt = false
158 sfhpy_all = true
159 lineages_csv = ("${params.db_root}"
160 + File.separator
161 + "taxonomy"
162 + File.separator
163 + "${params.db_mode}"
164 + File.separator
165 + "lineages.csv")
166 gsalkronapy_run = true
167 gsalkronapy_sf = 10000
168 gsalkronapy_smres_suffix = false
169 gsalkronapy_failed_suffix = false
170 gsalkronapy_num_lin_cols = false
171 gsalkronapy_lin_regex = false
172 krona_ktIT_run = true
173 krona_ktIT_n = 'all'
174 krona_ktIT_q = false
175 krona_ktIT_c = false
176 krona_res_suffix = '.krona.tsv'
177 fq_filter_by_len = 0
178 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
179 fq2_suffix = '_R2_001.fastq.gz'
180 }