Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/workflows/conf/bettercallsal.config @ 0:801b85b03a17 draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 params {
2 workflow_conceived_by = 'Kranti Konganti'
3 workflow_built_by = 'Kranti Konganti'
4 workflow_version = '1.0.0'
5 bcs_root_dbdir = '/server/galaxy/tool-data/bettercallsal-db/PDG000000002.3082'
6 bcs_db_mode = 'snp'
7 bcs_db_mode_index = (params.bcs_db_mode ==~ /snp/ ? '_cluster' : '_serotype')
8 bcs_thresholds = 'strict'
9 bcs_concat_pe = true
10 bbmerge_run = (params.bcs_concat_pe ? false : true)
11 bbmerge_adapters = false
12 bbmerge_reads = -1
13 bbmerge_ziplevel = 1
14 bbmerge_ordered = false
15 bbmerge_qtrim = true
16 bbmerge_qtrim2 = false
17 bbmerge_trimq = 10
18 bbmerge_minlength = 1
19 bbmerge_tbo = false
20 bbmerge_minavgquality = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
21 bbmerge_trimpolya = true
22 bbmerge_pfilter = (params.bcs_thresholds ==~ /strict/ ? 1 : false)
23 bbmerge_ouq = false
24 bbmerge_owq = true
25 bbmerge_strict = false
26 bbmerge_verystrict = false
27 bbmerge_ultrastrict = (params.bcs_thresholds ==~ /strict/ ? true : false)
28 bbmerge_maxstrict = false
29 bbmerge_loose = false
30 bbmerge_veryloose = false
31 bbmerge_ultraloose = false
32 bbmerge_maxloose = false
33 bbmerge_fast = false
34 bbmerge_k = 60
35 bbmerge_prealloc = true
36 fastp_run = true
37 fastp_failed_out = false
38 fastp_merged_out = false
39 fastp_overlapped_out = false
40 fastp_6 = false
41 fastp_reads_to_process = 0
42 fastp_fix_mgi_id = false
43 fastp_A = false
44 fastp_f = 0
45 fastp_t = 0
46 fastp_b = 0
47 fastp_F = 0
48 fastp_T = 0
49 fastp_B = 0
50 fastp_dedup = true
51 fastp_dup_calc_accuracy = 6
52 fastp_poly_g_min_len = 10
53 fastp_G = true
54 fastp_x = false
55 fastp_poly_x_min_len = 10
56 fastp_cut_front = true
57 fastp_cut_tail = false
58 fastp_cut_right = true
59 fastp_W = 20
60 fastp_M = 30
61 fastp_q = 30
62 fastp_u = 40
63 fastp_n = 5
64 fastp_e = 0
65 fastp_l = 35
66 fastp_max_len = 0
67 fastp_y = true
68 fastp_Y = 30
69 fastp_U = false
70 fastp_umi_loc = false
71 fastp_umi_len = false
72 fastp_umi_prefix = false
73 fastp_umi_skip = false
74 fastp_p = true
75 fastp_P = 20
76 fastp_use_custom_adapters = false
77 fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
78 + File.separator
79 + 'assets'
80 + File.separator
81 + 'adaptors.fa' : false)
82 mashscreen_run = true
83 mash_sketch = (params.bcs_root_dbdir
84 + File.separator
85 + 'mash_sketch'
86 + File.separator
87 + 'msh.k21.1000h.'
88 + params.bcs_db_mode
89 + '.msh')
90 mashscreen_w = false
91 mashscreen_i = false
92 mashscreen_v = false
93 tuspy_run = true
94 tuspy_s = false
95 tuspy_m = false
96 tuspy_ps = (params.bcs_root_dbdir
97 + File.separator
98 + 'index_metadata'
99 + File.separator
100 + 'per_'
101 + params.bcs_db_mode
102 + params.bcs_db_mode_index
103 + '.ACC2SERO.pickle')
104 tuspy_gd = (params.bcs_root_dbdir
105 + File.separator
106 + 'scaffold_genomes')
107 tuspy_gds = '_scaffolded_genomic.fna.gz'
108 tuspy_n = 10
109 tuspy_skip = 'PRJNA766315,PRJNA675435,PRJNA831577,PRJNA855361'
110 sourmashsketch_run = true
111 sourmashsketch_mode = 'dna'
112 sourmashsketch_file = false
113 sourmashsketch_f = false
114 sourmashsketch_merge = false
115 sourmashsketch_name = false
116 sourmashsketch_p = 'abund,scaled=1000,k=51,k=61,k=71'
117 sourmashsketch_singleton = true
118 sourmashsketch_randomize = false
119 sourmashgather_run = (params.sourmashsketch_run ?: false)
120 sourmashgather_n = false
121 sourmashgather_thr_bp = false
122 sourmashgather_ignoreabn = false
123 sourmashgather_prefetch = false
124 sourmashgather_noprefetch = false
125 sourmashgather_ani_ci = true
126 sourmashgather_k = 71
127 sourmashgather_protein = false
128 sourmashgather_noprotein = false
129 sourmashgather_dayhoff = false
130 sourmashgather_nodayhoff = false
131 sourmashgather_hp = false
132 sourmashgather_nohp = false
133 sourmashgather_dna = true
134 sourmashgather_nodna = false
135 sourmashgather_scaled = false
136 sourmashgather_inc_pat = false
137 sourmashgather_exc_pat = false
138 sourmashsearch_run = (params.sourmashsketch_run && !params.sourmashgather_run ?: false)
139 sourmashsearch_n = false
140 sourmashsearch_thr = '0'
141 sourmashsearch_contain = false
142 sourmashsearch_maxcontain = true
143 sourmashsearch_ignoreabn = true
144 sourmashsearch_ani_ci = false
145 sourmashsearch_k = 71
146 sourmashsearch_protein = false
147 sourmashsearch_noprotein = false
148 sourmashsearch_dayhoff = false
149 sourmashsearch_nodayhoff = false
150 sourmashsearch_hp = false
151 sourmashsearch_nohp = false
152 sourmashsearch_dna = true
153 sourmashsearch_nodna = false
154 sourmashsearch_scaled = false
155 sourmashsearch_inc_pat = false
156 sourmashsearch_exc_pat = false
157 sfhpy_run = true
158 sfhpy_fcn = (params.sourmashsearch_run ? 'similarity' : 'f_match')
159 sfhpy_fcv = (params.sourmashsearch_run ? 0.9 : 0.1)
160 sfhpy_gt = true
161 sfhpy_lt = false
162 kmaindex_run = true
163 kmaindex_t_db = false
164 kmaindex_k = 31
165 kmaindex_m = false
166 kmaindex_hc = false
167 kmaindex_ML = false
168 kmaindex_ME = false
169 kmaindex_Sparse = false
170 kmaindex_ht = false
171 kmaindex_hq = false
172 kmaindex_and = false
173 kmaindex_nbp = false
174 kmaalign_run = true
175 kmaalign_ignorequals = false
176 kmaalign_int = false
177 kmaalign_ef = false
178 kmaalign_vcf = false
179 kmaalign_sam = false
180 kmaalign_nc = true
181 kmaalign_na = true
182 kmaalign_nf = false
183 kmaalign_a = false
184 kmaalign_and = true
185 kmaalign_oa = false
186 kmaalign_bc = false
187 kmaalign_bcNano = false
188 kmaalign_bcd = false
189 kmaalign_bcg = false
190 kmaalign_ID = (params.bcs_thresholds ==~ /strict/ ? 10.0 : 5.0)
191 kmaalign_md = false
192 kmaalign_dense = false
193 kmaalign_ref_fsa = false
194 kmaalign_Mt1 = false
195 kmaalign_1t1 = false
196 kmaalign_mrs = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
197 kmaalign_mrc = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
198 kmaalign_mp = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
199 kmaalign_eq = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
200 kmaalign_mp = (params.kmaalign_ignorequals ? 0 : params.kmaalign_mp)
201 kmaalign_eq = (params.kmaalign_ignorequals ? 0 : params.kmaalign_eq)
202 kmaalign_mq = false
203 kmaalign_5p = false
204 kmaalign_3p = false
205 kmaalign_apm = false
206 kmaalign_cge = false
207 kmaalign_mrs = (params.sourmashgather_run ? false : params.kmaalign_mrs)
208 kmaalign_and = (params.sourmashgather_run ? false : true)
209 kmaalign_ID = (params.sourmashgather_run ? false : params.kmaalign_ID)
210 megahit_run = true
211 megahit_min_count = false
212 megahit_k_list = false
213 megahit_no_mercy = false
214 megahit_bubble_level = false
215 megahit_merge_level = false
216 megahit_prune_level = false
217 megahit_prune_depth = false
218 megahit_low_local_ratio = false
219 megahit_max_tip_len = false
220 megahit_no_local = false
221 megahit_kmin_1pass = false
222 megahit_preset = 'meta-sensitive'
223 megahit_mem_flag = 2
224 megahit_min_contig_len = false
225 mlst_run = true
226 mlst_scheme = 'senterica_achtman_2'
227 mlst_legacy = true
228 mlst_minid = 95
229 mlst_mincov = 10
230 mlst_minscore = 50
231 abricate_run = true
232 abricate_datadir = ("${projectDir}"
233 + File.separator
234 + 'assets'
235 + File.separator
236 + 'abricate_dbs')
237 abricate_minid = 90
238 abricate_mincov = 80
239 abricate_summary_run = true
240 salmonidx_run = true
241 salmonidx_k = false
242 salmonidx_gencode = false
243 salmonidx_features = false
244 salmonidx_keepDuplicates = false
245 salmonidx_keepFixedFasta = false
246 salmonidx_filterSize = false
247 salmonidx_sparse = false
248 salmonidx_n = false
249 salmonidx_decoys = false
250 salmonalign_libtype = 'SF'
251 gsrpy_run = true
252 gsrpy_url = true
253 gsrpy_snp_clus_metadata = (params.bcs_root_dbdir
254 + File.separator
255 + 'download_pdg_metadata'
256 + File.separator
257 + getPDGRelease(params.bcs_root_dbdir)
258 + File.separator
259 + getPDGRelease(params.bcs_root_dbdir)
260 + '.reference_target.cluster_list.tsv')
261 sourmashcompare_mode = 'ani,containment'
262 fq_filter_by_len = 0
263 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
264 fq2_suffix = '_R2_001.fastq.gz'
265 multiqc_run = true
266 }
267
268 /*
269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
270 METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
271 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
272 */
273
274 def getPDGRelease(db_path) {
275 db_path_obj = new File( db_path )
276 def pdg_release = []
277
278 db_path_obj.eachDirRecurse {
279 it.toString() =~ /PDG/ \
280 ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
281 : null
282 }
283
284 return pdg_release.unique().join('').toString()
285 }