Mercurial > repos > kkonganti > cfsan_cronology

comparison 0.2.0/workflows/conf/cronology.config @ 11:a5f31c44f8c9

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planemo upload
author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
1 params {
2 workflow_conceived_by = 'Kranti Konganti'
3 workflow_built_by = 'Kranti Konganti'
4 workflow_version = '0.2.0'
5 ref_acc = 'GCF_003516125'
6 cronology_root_dbdir = '/galaxy/cfsan-centriflaken-db/cronology/PDG000000043.213'
7 upload_microreact = true
8 microreact_api_key = ("${projectDir}"
9 + File.separator
10 + 'assets'
11 + File.separator
12 + 'microreact_api.key')
13 microreact_tree_name = 'cronology_run_tree'
14 dpubmlstpy_run = true
15 dpubmlstpy_org = 'cronobacter'
16 dpubmlstpy_mlsts = 'schemes/1'
17 dpubmlstpy_profile = false
18 dpubmlstpy_loci = false
19 dpubmlstpy_suffix = false
20 dpubmlstpy_akey = false
21 dpubmlstpy_id = false
22 fastp_run = true
23 fastp_failed_out = false
24 fastp_merged_out = false
25 fastp_overlapped_out = false
26 fastp_6 = false
27 fastp_reads_to_process = 0
28 fastp_fix_mgi_id = false
29 fastp_A = false
30 fastp_f = 0
31 fastp_t = 0
32 fastp_b = 0
33 fastp_F = 0
34 fastp_T = 0
35 fastp_B = 0
36 fastp_dedup = true
37 fastp_dup_calc_accuracy = 6
38 fastp_poly_g_min_len = 10
39 fastp_G = true
40 fastp_x = false
41 fastp_poly_x_min_len = 10
42 fastp_cut_front = true
43 fastp_cut_tail = false
44 fastp_cut_right = true
45 fastp_W = 20
46 fastp_M = 30
47 fastp_q = 30
48 fastp_u = 40
49 fastp_n = 5
50 fastp_e = 0
51 fastp_l = 35
52 fastp_max_len = 0
53 fastp_y = true
54 fastp_Y = 30
55 fastp_U = false
56 fastp_umi_loc = false
57 fastp_umi_len = false
58 fastp_umi_prefix = false
59 fastp_umi_skip = false
60 fastp_p = true
61 fastp_P = 20
62 fastp_use_custom_adapters = false
63 fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
64 + File.separator
65 + 'assets'
66 + File.separator
67 + 'adaptors.fa' : false)
68 mashscreen_w = false
69 mashscreen_i = false
70 mashscreen_v = false
71 tuspy_run = true
72 tuspy_s = false
73 tuspy_m = false
74 tuspy_ps = (params.cronology_root_dbdir
75 + File.separator
76 + 'index_pdg_metadata'
77 + File.separator
78 + 'IDXD_PDG_METAD.pickle')
79 tuspy_gd = (params.cronology_root_dbdir
80 + File.separator
81 + 'scaffold_genomes')
82 tuspy_gds = '_scaffolded_genomic.fna.gz'
83 tuspy_n = 5
84 spades_run = false
85 spades_isolate = false
86 spades_sc = false
87 spades_meta = true
88 spades_bio = false
89 spades_corona = false
90 spades_rna = false
91 spades_plasmid = false
92 spades_metaviral = false
93 spades_metaplasmid = false
94 spades_rnaviral = false
95 spades_iontorrent = false
96 spades_only_assembler = false
97 spades_careful = false
98 spades_cov_cutoff = false
99 spades_k = false
100 spades_hmm = false
101 shovill_run = true
102 shovill_depth = 150
103 shovill_gsize = false
104 shovill_minlen = 200
105 shovill_mincov = 5
106 shovill_namefmt = false
107 shovill_keepfiles = false
108 shovill_assembler = false
109 shovill_opts = false
110 shovill_kmers = false
111 shovill_trim = false
112 shovill_noreadcorr = false
113 shovill_nostitch = false
114 shovill_nocorr = false
115 polypolish_run = true
116 polypolish_d = 5
117 polypolish_i = 0.2
118 polypolish_m = 10
119 polypolish_v = 0.5
120 mashtree_run = true
121 mashtree_fofn = true
122 mashtree_trunclength = false
123 mashtree_mindepth = false
124 mashtree_kmerlength = false
125 mashtree_sketchsize = false
126 mashtree_seed = false
127 mashtree_genomesize = false
128 mashtree_sigfigs = false
129 mashtree_sortorder = false
130 quast_run = true
131 quast_min_contig = 200
132 quast_split_scaffolds = false
133 quast_euk = false
134 quast_fungal = false
135 quast_large = false
136 quast_k = false
137 quast_kmer_size = false
138 quast_circos = true
139 quast_glimmer = true
140 quast_gene_thr = '0,300,1500,3000'
141 quast_rna_finding = true
142 quast_ref_size = false
143 quast_ctg_thr = '0,1000,5000,10000,25000,50000'
144 quast_x_for_nx = 90
145 quast_use_all_alns = false
146 quast_min_alignment = 65
147 quast_min_identity = '95.0'
148 quast_ambig_usage = 'one'
149 quast_ambig_score = '0.99'
150 quast_strict_na = false
151 quast_x = 1000
152 quast_local_mis_size = 200
153 quast_sca_gap_size = 10000
154 quast_unaln_part_size = 500
155 quast_skip_unaln_mis_ctgs = false
156 quast_fragmented = false
157 quast_frag_max_ident = (params.quast_fragmented ? 200 : false)
158 quast_plots_format = 'pdf'
159 prodka_run = true
160 prodigal_run = (params.prodka_run ?: false)
161 prodigal_c = false
162 prodigal_f = 'gbk'
163 prodigal_g = 11
164 prodigal_m = true
165 prodigal_n = false
166 prodigal_p = 'single'
167 prodigal_t = true
168 prokka_run = (params.prodka_run ?: false)
169 prokka_dbdir = false
170 prokka_addgenes = true
171 prokka_addmrna = true
172 prokka_locustag = false
173 prokka_increment = false
174 prokka_gffver = false
175 prokka_compliant = true
176 prokka_centre = 'CFSAN-FDA'
177 prokka_accver = false
178 prokka_genus = (params.dpubmlstpy_org.capitalize() ?: 'Cronobacter')
179 prokka_species = false
180 prokka_strain = false
181 prokka_plasmid = false
182 prokka_kingdom = false
183 prokka_gcode = false
184 prokka_usegenus = true
185 prokka_metagenome = false
186 prokka_rawproduct = false
187 prokka_cdsrnaolap = false
188 prokka_evalue = '1e-9'
189 prokka_coverage = 80
190 prokka_fast = false
191 prokka_noanno = false
192 prokka_mincontiglen = 200
193 prokka_rfam = false
194 prokka_norrna = false
195 prokka_notrna = false
196 prokka_rnammer = false
197 pirate_run = false
198 pirate_steps = false
199 pirate_features = false
200 pirate_nucl = false
201 pirate_pan_opt = "'--diamond'"
202 pirate_pan_off = false
203 pirate_min_len = 200
204 pirate_para_off = false
205 pirate_para_args = false
206 pirate_classify_off = false
207 pirate_align = false
208 pirate_rplots = false
209 mashscreen_run = true
210 mash_sketch = (params.cronology_root_dbdir
211 + File.separator
212 + 'mash_paste'
213 + File.separator
214 + 'msh.k21.1000h.'
215 + getPDGRelease(params.cronology_root_dbdir)
216 + '.msh')
217 mlst_run = true
218 mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
219 mlst_legacy = true
220 mlst_minid = 95
221 mlst_mincov = 10
222 mlst_minscore = 50
223 mlst_blastdb = false
224 mlst_datadir = false
225 mlst_label = true
226 abricate_run = true
227 abricate_datadir = ("${projectDir}"
228 + File.separator
229 + 'assets'
230 + File.separator
231 + 'abricate_dbs')
232 abricate_minid = 90
233 abricate_mincov = 80
234 abricate_summary_run = true
235 fq_filter_by_len = 0
236 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
237 fq2_suffix = '_R2_001.fastq.gz'
238 }
239
240 /*
241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
242 METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
244 */
245
246 def getPDGRelease(db_path) {
247 db_path_obj = new File( db_path )
248 def pdg_release = []
249
250 db_path_obj.eachDirRecurse {
251 it.toString() =~ /PDG/ \
252 ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
253 : null
254 }
255
256 return pdg_release.unique().join('').toString()
257 }