Mercurial > repos > kkonganti > cfsan_cronology

comparison 0.1.0/workflows/conf/cronology.config @ 0:c8597e9e1a97

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
parents
children 7ac696717239
comparison
equal deleted inserted replaced
-1:000000000000 0:c8597e9e1a97
1 params {
2 workflow_conceived_by = 'Kranti Konganti'
3 workflow_built_by = 'Kranti Konganti'
4 workflow_version = '0.1.0'
5 ref_acc = 'GCF_003516125'
6 cronology_root_dbdir = '/hpc/scratch/Kranti.Konganti/trash/cronobacter/test_nf_db'
7 dpubmlstpy_run = true
8 dpubmlstpy_org = 'cronobacter'
9 dpubmlstpy_mlsts = 'schemes/1'
10 dpubmlstpy_profile = false
11 dpubmlstpy_loci = false
12 dpubmlstpy_suffix = false
13 dpubmlstpy_akey = false
14 dpubmlstpy_id = false
15 fastp_run = true
16 fastp_failed_out = false
17 fastp_merged_out = false
18 fastp_overlapped_out = false
19 fastp_6 = false
20 fastp_reads_to_process = 0
21 fastp_fix_mgi_id = false
22 fastp_A = false
23 fastp_f = 0
24 fastp_t = 0
25 fastp_b = 0
26 fastp_F = 0
27 fastp_T = 0
28 fastp_B = 0
29 fastp_dedup = true
30 fastp_dup_calc_accuracy = 6
31 fastp_poly_g_min_len = 10
32 fastp_G = true
33 fastp_x = false
34 fastp_poly_x_min_len = 10
35 fastp_cut_front = true
36 fastp_cut_tail = false
37 fastp_cut_right = true
38 fastp_W = 20
39 fastp_M = 30
40 fastp_q = 30
41 fastp_u = 40
42 fastp_n = 5
43 fastp_e = 0
44 fastp_l = 35
45 fastp_max_len = 0
46 fastp_y = true
47 fastp_Y = 30
48 fastp_U = false
49 fastp_umi_loc = false
50 fastp_umi_len = false
51 fastp_umi_prefix = false
52 fastp_umi_skip = false
53 fastp_p = true
54 fastp_P = 20
55 fastp_use_custom_adapters = false
56 fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
57 + File.separator
58 + 'assets'
59 + File.separator
60 + 'adaptors.fa' : false)
61 mashscreen_w = false
62 mashscreen_i = false
63 mashscreen_v = false
64 tuspy_run = true
65 tuspy_s = false
66 tuspy_m = false
67 tuspy_ps = (params.cronology_root_dbdir
68 + File.separator
69 + 'index_pdg_metadata'
70 + File.separator
71 + 'IDXD_PDG_METAD.pickle')
72 tuspy_gd = (params.cronology_root_dbdir
73 + File.separator
74 + 'scaffold_genomes')
75 tuspy_gds = '_scaffolded_genomic.fna.gz'
76 tuspy_n = 5
77 spades_run = false
78 spades_isolate = false
79 spades_sc = false
80 spades_meta = true
81 spades_bio = false
82 spades_corona = false
83 spades_rna = false
84 spades_plasmid = false
85 spades_metaviral = false
86 spades_metaplasmid = false
87 spades_rnaviral = false
88 spades_iontorrent = false
89 spades_only_assembler = false
90 spades_careful = false
91 spades_cov_cutoff = false
92 spades_k = false
93 spades_hmm = false
94 shovill_run = true
95 shovill_depth = 150
96 shovill_gsize = false
97 shovill_minlen = 200
98 shovill_mincov = 5
99 shovill_namefmt = false
100 shovill_keepfiles = false
101 shovill_assembler = false
102 shovill_opts = false
103 shovill_kmers = false
104 shovill_trim = false
105 shovill_noreadcorr = false
106 shovill_nostitch = false
107 shovill_nocorr = false
108 polypolish_run = true
109 polypolish_d = 5
110 polypolish_i = 0.2
111 polypolish_m = 10
112 polypolish_v = 0.5
113 mashtree_run = true
114 mashtree_fofn = true
115 mashtree_trunclength = false
116 mashtree_mindepth = false
117 mashtree_kmerlength = false
118 mashtree_sketchsize = false
119 mashtree_seed = false
120 mashtree_genomesize = false
121 mashtree_sigfigs = false
122 mashtree_sortorder = false
123 quast_run = true
124 quast_min_contig = 200
125 quast_split_scaffolds = false
126 quast_euk = false
127 quast_fungal = false
128 quast_large = false
129 quast_k = false
130 quast_kmer_size = false
131 quast_circos = true
132 quast_glimmer = true
133 quast_gene_thr = '0,300,1500,3000'
134 quast_rna_finding = true
135 quast_ref_size = false
136 quast_ctg_thr = '0,1000,5000,10000,25000,50000'
137 quast_x_for_nx = 90
138 quast_use_all_alns = false
139 quast_min_alignment = 65
140 quast_min_identity = '95.0'
141 quast_ambig_usage = 'one'
142 quast_ambig_score = '0.99'
143 quast_strict_na = false
144 quast_x = 1000
145 quast_local_mis_size = 200
146 quast_sca_gap_size = 10000
147 quast_unaln_part_size = 500
148 quast_skip_unaln_mis_ctgs = false
149 quast_fragmented = false
150 quast_frag_max_ident = (params.quast_fragmented ? 200 : false)
151 quast_plots_format = 'pdf'
152 prodka_run = true
153 prodigal_run = (params.prodka_run ?: false)
154 prodigal_c = false
155 prodigal_f = 'gbk'
156 prodigal_g = 11
157 prodigal_m = true
158 prodigal_n = false
159 prodigal_p = 'single'
160 prodigal_t = true
161 prokka_run = (params.prodka_run ?: false)
162 prokka_dbdir = false
163 prokka_addgenes = true
164 prokka_addmrna = true
165 prokka_locustag = false
166 prokka_increment = false
167 prokka_gffver = false
168 prokka_compliant = true
169 prokka_centre = 'CFSAN-FDA'
170 prokka_accver = false
171 prokka_genus = (params.dpubmlstpy_org.capitalize() ?: 'Cronobacter')
172 prokka_species = false
173 prokka_strain = false
174 prokka_plasmid = false
175 prokka_kingdom = false
176 prokka_gcode = false
177 prokka_usegenus = true
178 prokka_metagenome = false
179 prokka_rawproduct = false
180 prokka_cdsrnaolap = false
181 prokka_evalue = '1e-9'
182 prokka_coverage = 80
183 prokka_fast = false
184 prokka_noanno = false
185 prokka_mincontiglen = 200
186 prokka_rfam = false
187 prokka_norrna = false
188 prokka_notrna = false
189 prokka_rnammer = false
190 pirate_run = false
191 pirate_steps = false
192 pirate_features = false
193 pirate_nucl = false
194 pirate_pan_opt = "'--diamond'"
195 pirate_pan_off = false
196 pirate_min_len = 200
197 pirate_para_off = false
198 pirate_para_args = false
199 pirate_classify_off = false
200 pirate_align = false
201 pirate_rplots = false
202 mashscreen_run = true
203 mash_sketch = (params.cronology_root_dbdir
204 + File.separator
205 + 'mash_paste'
206 + File.separator
207 + 'msh.k21.1000h.'
208 + getPDGRelease(params.cronology_root_dbdir)
209 + '.msh')
210 mlst_run = true
211 mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
212 mlst_legacy = true
213 mlst_minid = 95
214 mlst_mincov = 10
215 mlst_minscore = 50
216 mlst_blastdb = false
217 mlst_datadir = false
218 mlst_label = true
219 abricate_run = true
220 abricate_datadir = ("${projectDir}"
221 + File.separator
222 + 'assets'
223 + File.separator
224 + 'abricate_dbs')
225 abricate_minid = 90
226 abricate_mincov = 80
227 abricate_summary_run = true
228 fq_filter_by_len = 0
229 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
230 fq2_suffix = '_R2_001.fastq.gz'
231 }
232
233 /*
234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
235 METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
236 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
237 */
238
239 def getPDGRelease(db_path) {
240 db_path_obj = new File( db_path )
241 def pdg_release = []
242
243 db_path_obj.eachDirRecurse {
244 it.toString() =~ /PDG/ \
245 ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
246 : null
247 }
248
249 return pdg_release.unique().join('').toString()
250 }