|
kkonganti@11
|
1 params {
|
|
kkonganti@11
|
2 workflow_conceived_by = 'Kranti Konganti'
|
|
kkonganti@11
|
3 workflow_built_by = 'Kranti Konganti'
|
|
kkonganti@11
|
4 workflow_version = '0.6.1'
|
|
kkonganti@11
|
5 bcs_root_dbdir = '/hpc/db/bettercallsal/latest'
|
|
kkonganti@11
|
6 bcs_db_mode = 'snp'
|
|
kkonganti@11
|
7 bcs_db_mode_index = (params.bcs_db_mode ==~ /snp/ ? '_cluster' : '_serotype')
|
|
kkonganti@11
|
8 bcs_thresholds = 'strict'
|
|
kkonganti@11
|
9 bcs_concat_pe = true
|
|
kkonganti@11
|
10 bbmerge_run = (params.bcs_concat_pe ? false : true)
|
|
kkonganti@11
|
11 bbmerge_adapters = false
|
|
kkonganti@11
|
12 bbmerge_reads = -1
|
|
kkonganti@11
|
13 bbmerge_ziplevel = 1
|
|
kkonganti@11
|
14 bbmerge_ordered = false
|
|
kkonganti@11
|
15 bbmerge_qtrim = true
|
|
kkonganti@11
|
16 bbmerge_qtrim2 = false
|
|
kkonganti@11
|
17 bbmerge_trimq = 10
|
|
kkonganti@11
|
18 bbmerge_minlength = 1
|
|
kkonganti@11
|
19 bbmerge_tbo = false
|
|
kkonganti@11
|
20 bbmerge_minavgquality = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
|
|
kkonganti@11
|
21 bbmerge_trimpolya = true
|
|
kkonganti@11
|
22 bbmerge_pfilter = (params.bcs_thresholds ==~ /strict/ ? 1 : false)
|
|
kkonganti@11
|
23 bbmerge_ouq = false
|
|
kkonganti@11
|
24 bbmerge_owq = true
|
|
kkonganti@11
|
25 bbmerge_strict = false
|
|
kkonganti@11
|
26 bbmerge_verystrict = false
|
|
kkonganti@11
|
27 bbmerge_ultrastrict = (params.bcs_thresholds ==~ /strict/ ? true : false)
|
|
kkonganti@11
|
28 bbmerge_maxstrict = false
|
|
kkonganti@11
|
29 bbmerge_loose = false
|
|
kkonganti@11
|
30 bbmerge_veryloose = false
|
|
kkonganti@11
|
31 bbmerge_ultraloose = false
|
|
kkonganti@11
|
32 bbmerge_maxloose = false
|
|
kkonganti@11
|
33 bbmerge_fast = false
|
|
kkonganti@11
|
34 bbmerge_k = 60
|
|
kkonganti@11
|
35 bbmerge_prealloc = true
|
|
kkonganti@11
|
36 fastp_run = true
|
|
kkonganti@11
|
37 fastp_failed_out = false
|
|
kkonganti@11
|
38 fastp_merged_out = false
|
|
kkonganti@11
|
39 fastp_overlapped_out = false
|
|
kkonganti@11
|
40 fastp_6 = false
|
|
kkonganti@11
|
41 fastp_reads_to_process = 0
|
|
kkonganti@11
|
42 fastp_fix_mgi_id = false
|
|
kkonganti@11
|
43 fastp_A = false
|
|
kkonganti@11
|
44 fastp_f = 0
|
|
kkonganti@11
|
45 fastp_t = 0
|
|
kkonganti@11
|
46 fastp_b = 0
|
|
kkonganti@11
|
47 fastp_F = 0
|
|
kkonganti@11
|
48 fastp_T = 0
|
|
kkonganti@11
|
49 fastp_B = 0
|
|
kkonganti@11
|
50 fastp_dedup = true
|
|
kkonganti@11
|
51 fastp_dup_calc_accuracy = 6
|
|
kkonganti@11
|
52 fastp_poly_g_min_len = 10
|
|
kkonganti@11
|
53 fastp_G = true
|
|
kkonganti@11
|
54 fastp_x = false
|
|
kkonganti@11
|
55 fastp_poly_x_min_len = 10
|
|
kkonganti@11
|
56 fastp_cut_front = true
|
|
kkonganti@11
|
57 fastp_cut_tail = false
|
|
kkonganti@11
|
58 fastp_cut_right = true
|
|
kkonganti@11
|
59 fastp_W = 20
|
|
kkonganti@11
|
60 fastp_M = 30
|
|
kkonganti@11
|
61 fastp_q = 30
|
|
kkonganti@11
|
62 fastp_u = 40
|
|
kkonganti@11
|
63 fastp_n = 5
|
|
kkonganti@11
|
64 fastp_e = 0
|
|
kkonganti@11
|
65 fastp_l = 35
|
|
kkonganti@11
|
66 fastp_max_len = 0
|
|
kkonganti@11
|
67 fastp_y = true
|
|
kkonganti@11
|
68 fastp_Y = 30
|
|
kkonganti@11
|
69 fastp_U = false
|
|
kkonganti@11
|
70 fastp_umi_loc = false
|
|
kkonganti@11
|
71 fastp_umi_len = false
|
|
kkonganti@11
|
72 fastp_umi_prefix = false
|
|
kkonganti@11
|
73 fastp_umi_skip = false
|
|
kkonganti@11
|
74 fastp_p = true
|
|
kkonganti@11
|
75 fastp_P = 20
|
|
kkonganti@11
|
76 fastp_use_custom_adapters = false
|
|
kkonganti@11
|
77 fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
|
|
kkonganti@11
|
78 + File.separator
|
|
kkonganti@11
|
79 + 'assets'
|
|
kkonganti@11
|
80 + File.separator
|
|
kkonganti@11
|
81 + 'adaptors.fa' : false)
|
|
kkonganti@11
|
82 mashscreen_run = true
|
|
kkonganti@11
|
83 mash_sketch = (params.bcs_root_dbdir
|
|
kkonganti@11
|
84 + File.separator
|
|
kkonganti@11
|
85 + 'mash_sketch'
|
|
kkonganti@11
|
86 + File.separator
|
|
kkonganti@11
|
87 + 'msh.k21.1000h.'
|
|
kkonganti@11
|
88 + params.bcs_db_mode
|
|
kkonganti@11
|
89 + '.msh')
|
|
kkonganti@11
|
90 mashscreen_w = false
|
|
kkonganti@11
|
91 mashscreen_i = false
|
|
kkonganti@11
|
92 mashscreen_v = false
|
|
kkonganti@11
|
93 tuspy_run = true
|
|
kkonganti@11
|
94 tuspy_s = false
|
|
kkonganti@11
|
95 tuspy_m = false
|
|
kkonganti@11
|
96 tuspy_ps = (params.bcs_root_dbdir
|
|
kkonganti@11
|
97 + File.separator
|
|
kkonganti@11
|
98 + 'index_metadata'
|
|
kkonganti@11
|
99 + File.separator
|
|
kkonganti@11
|
100 + 'per_'
|
|
kkonganti@11
|
101 + params.bcs_db_mode
|
|
kkonganti@11
|
102 + params.bcs_db_mode_index
|
|
kkonganti@11
|
103 + '.ACC2SERO.pickle')
|
|
kkonganti@11
|
104 tuspy_gd = (params.bcs_root_dbdir
|
|
kkonganti@11
|
105 + File.separator
|
|
kkonganti@11
|
106 + 'scaffold_genomes')
|
|
kkonganti@11
|
107 tuspy_gds = '_scaffolded_genomic.fna.gz'
|
|
kkonganti@11
|
108 tuspy_n = 10
|
|
kkonganti@11
|
109 sourmashsketch_run = true
|
|
kkonganti@11
|
110 sourmashsketch_mode = 'dna'
|
|
kkonganti@11
|
111 sourmashsketch_file = false
|
|
kkonganti@11
|
112 sourmashsketch_f = false
|
|
kkonganti@11
|
113 sourmashsketch_merge = false
|
|
kkonganti@11
|
114 sourmashsketch_name = false
|
|
kkonganti@11
|
115 sourmashsketch_p = 'abund,scaled=1000,k=51,k=61,k=71'
|
|
kkonganti@11
|
116 sourmashsketch_singleton = true
|
|
kkonganti@11
|
117 sourmashsketch_randomize = false
|
|
kkonganti@11
|
118 sourmashgather_run = (params.sourmashsketch_run ?: false)
|
|
kkonganti@11
|
119 sourmashgather_n = false
|
|
kkonganti@11
|
120 sourmashgather_thr_bp = false
|
|
kkonganti@11
|
121 sourmashgather_ignoreabn = false
|
|
kkonganti@11
|
122 sourmashgather_prefetch = false
|
|
kkonganti@11
|
123 sourmashgather_noprefetch = false
|
|
kkonganti@11
|
124 sourmashgather_ani_ci = true
|
|
kkonganti@11
|
125 sourmashgather_k = 71
|
|
kkonganti@11
|
126 sourmashgather_protein = false
|
|
kkonganti@11
|
127 sourmashgather_noprotein = false
|
|
kkonganti@11
|
128 sourmashgather_dayhoff = false
|
|
kkonganti@11
|
129 sourmashgather_nodayhoff = false
|
|
kkonganti@11
|
130 sourmashgather_hp = false
|
|
kkonganti@11
|
131 sourmashgather_nohp = false
|
|
kkonganti@11
|
132 sourmashgather_dna = true
|
|
kkonganti@11
|
133 sourmashgather_nodna = false
|
|
kkonganti@11
|
134 sourmashgather_scaled = false
|
|
kkonganti@11
|
135 sourmashgather_inc_pat = false
|
|
kkonganti@11
|
136 sourmashgather_exc_pat = false
|
|
kkonganti@11
|
137 sourmashsearch_run = (params.sourmashsketch_run && !params.sourmashgather_run ?: false)
|
|
kkonganti@11
|
138 sourmashsearch_n = false
|
|
kkonganti@11
|
139 sourmashsearch_thr = '0'
|
|
kkonganti@11
|
140 sourmashsearch_contain = false
|
|
kkonganti@11
|
141 sourmashsearch_maxcontain = true
|
|
kkonganti@11
|
142 sourmashsearch_ignoreabn = true
|
|
kkonganti@11
|
143 sourmashsearch_ani_ci = false
|
|
kkonganti@11
|
144 sourmashsearch_k = 71
|
|
kkonganti@11
|
145 sourmashsearch_protein = false
|
|
kkonganti@11
|
146 sourmashsearch_noprotein = false
|
|
kkonganti@11
|
147 sourmashsearch_dayhoff = false
|
|
kkonganti@11
|
148 sourmashsearch_nodayhoff = false
|
|
kkonganti@11
|
149 sourmashsearch_hp = false
|
|
kkonganti@11
|
150 sourmashsearch_nohp = false
|
|
kkonganti@11
|
151 sourmashsearch_dna = true
|
|
kkonganti@11
|
152 sourmashsearch_nodna = false
|
|
kkonganti@11
|
153 sourmashsearch_scaled = false
|
|
kkonganti@11
|
154 sourmashsearch_inc_pat = false
|
|
kkonganti@11
|
155 sourmashsearch_exc_pat = false
|
|
kkonganti@11
|
156 sfhpy_run = true
|
|
kkonganti@11
|
157 sfhpy_fcn = (params.sourmashsearch_run ? 'similarity' : 'f_match')
|
|
kkonganti@11
|
158 sfhpy_fcv = (params.sourmashsearch_run ? 0.9 : 0.1)
|
|
kkonganti@11
|
159 sfhpy_gt = true
|
|
kkonganti@11
|
160 sfhpy_lt = false
|
|
kkonganti@11
|
161 kmaindex_run = true
|
|
kkonganti@11
|
162 kmaindex_t_db = false
|
|
kkonganti@11
|
163 kmaindex_k = 31
|
|
kkonganti@11
|
164 kmaindex_m = false
|
|
kkonganti@11
|
165 kmaindex_hc = false
|
|
kkonganti@11
|
166 kmaindex_ML = false
|
|
kkonganti@11
|
167 kmaindex_ME = false
|
|
kkonganti@11
|
168 kmaindex_Sparse = false
|
|
kkonganti@11
|
169 kmaindex_ht = false
|
|
kkonganti@11
|
170 kmaindex_hq = false
|
|
kkonganti@11
|
171 kmaindex_and = false
|
|
kkonganti@11
|
172 kmaindex_nbp = false
|
|
kkonganti@11
|
173 kmaalign_run = true
|
|
kkonganti@11
|
174 kmaalign_ignorequals = false
|
|
kkonganti@11
|
175 kmaalign_int = false
|
|
kkonganti@11
|
176 kmaalign_ef = false
|
|
kkonganti@11
|
177 kmaalign_vcf = false
|
|
kkonganti@11
|
178 kmaalign_sam = false
|
|
kkonganti@11
|
179 kmaalign_nc = true
|
|
kkonganti@11
|
180 kmaalign_na = true
|
|
kkonganti@11
|
181 kmaalign_nf = false
|
|
kkonganti@11
|
182 kmaalign_a = false
|
|
kkonganti@11
|
183 kmaalign_and = true
|
|
kkonganti@11
|
184 kmaalign_oa = false
|
|
kkonganti@11
|
185 kmaalign_bc = false
|
|
kkonganti@11
|
186 kmaalign_bcNano = false
|
|
kkonganti@11
|
187 kmaalign_bcd = false
|
|
kkonganti@11
|
188 kmaalign_bcg = false
|
|
kkonganti@11
|
189 kmaalign_ID = (params.bcs_thresholds ==~ /strict/ ? 10.0 : 5.0)
|
|
kkonganti@11
|
190 kmaalign_md = false
|
|
kkonganti@11
|
191 kmaalign_dense = false
|
|
kkonganti@11
|
192 kmaalign_ref_fsa = false
|
|
kkonganti@11
|
193 kmaalign_Mt1 = false
|
|
kkonganti@11
|
194 kmaalign_1t1 = false
|
|
kkonganti@11
|
195 kmaalign_mrs = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
|
|
kkonganti@11
|
196 kmaalign_mrc = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
|
|
kkonganti@11
|
197 kmaalign_mp = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
|
|
kkonganti@11
|
198 kmaalign_eq = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
|
|
kkonganti@11
|
199 kmaalign_mp = (params.kmaalign_ignorequals ? 0 : params.kmaalign_mp)
|
|
kkonganti@11
|
200 kmaalign_eq = (params.kmaalign_ignorequals ? 0 : params.kmaalign_eq)
|
|
kkonganti@11
|
201 kmaalign_mq = false
|
|
kkonganti@11
|
202 kmaalign_5p = false
|
|
kkonganti@11
|
203 kmaalign_3p = false
|
|
kkonganti@11
|
204 kmaalign_apm = false
|
|
kkonganti@11
|
205 kmaalign_cge = false
|
|
kkonganti@11
|
206 kmaalign_mrs = (params.sourmashgather_run ? false : params.kmaalign_mrs)
|
|
kkonganti@11
|
207 kmaalign_and = (params.sourmashgather_run ? false : true)
|
|
kkonganti@11
|
208 kmaalign_ID = (params.sourmashgather_run ? false : params.kmaalign_ID)
|
|
kkonganti@11
|
209 megahit_run = true
|
|
kkonganti@11
|
210 megahit_min_count = false
|
|
kkonganti@11
|
211 megahit_k_list = false
|
|
kkonganti@11
|
212 megahit_no_mercy = false
|
|
kkonganti@11
|
213 megahit_bubble_level = false
|
|
kkonganti@11
|
214 megahit_merge_level = false
|
|
kkonganti@11
|
215 megahit_prune_level = false
|
|
kkonganti@11
|
216 megahit_prune_depth = false
|
|
kkonganti@11
|
217 megahit_low_local_ratio = false
|
|
kkonganti@11
|
218 megahit_max_tip_len = false
|
|
kkonganti@11
|
219 megahit_no_local = false
|
|
kkonganti@11
|
220 megahit_kmin_1pass = false
|
|
kkonganti@11
|
221 megahit_preset = 'meta-sensitive'
|
|
kkonganti@11
|
222 megahit_mem_flag = 2
|
|
kkonganti@11
|
223 megahit_min_contig_len = false
|
|
kkonganti@11
|
224 mlst_run = true
|
|
kkonganti@11
|
225 mlst_scheme = 'senterica_achtman_2'
|
|
kkonganti@11
|
226 mlst_legacy = true
|
|
kkonganti@11
|
227 mlst_minid = 95
|
|
kkonganti@11
|
228 mlst_mincov = 10
|
|
kkonganti@11
|
229 mlst_minscore = 50
|
|
kkonganti@11
|
230 abricate_run = true
|
|
kkonganti@11
|
231 abricate_datadir = ("${projectDir}"
|
|
kkonganti@11
|
232 + File.separator
|
|
kkonganti@11
|
233 + 'assets'
|
|
kkonganti@11
|
234 + File.separator
|
|
kkonganti@11
|
235 + 'abricate_dbs')
|
|
kkonganti@11
|
236 abricate_minid = 90
|
|
kkonganti@11
|
237 abricate_mincov = 80
|
|
kkonganti@11
|
238 abricate_summary_run = true
|
|
kkonganti@11
|
239 salmonidx_run = true
|
|
kkonganti@11
|
240 salmonidx_k = false
|
|
kkonganti@11
|
241 salmonidx_gencode = false
|
|
kkonganti@11
|
242 salmonidx_features = false
|
|
kkonganti@11
|
243 salmonidx_keepDuplicates = false
|
|
kkonganti@11
|
244 salmonidx_keepFixedFasta = false
|
|
kkonganti@11
|
245 salmonidx_filterSize = false
|
|
kkonganti@11
|
246 salmonidx_sparse = false
|
|
kkonganti@11
|
247 salmonidx_n = false
|
|
kkonganti@11
|
248 salmonidx_decoys = false
|
|
kkonganti@11
|
249 salmonalign_libtype = 'SF'
|
|
kkonganti@11
|
250 gsrpy_run = true
|
|
kkonganti@11
|
251 gsrpy_url = true
|
|
kkonganti@11
|
252 gsrpy_snp_clus_metadata = (params.bcs_root_dbdir
|
|
kkonganti@11
|
253 + File.separator
|
|
kkonganti@11
|
254 + 'download_pdg_metadata'
|
|
kkonganti@11
|
255 + File.separator
|
|
kkonganti@11
|
256 + getPDGRelease(params.bcs_root_dbdir)
|
|
kkonganti@11
|
257 + File.separator
|
|
kkonganti@11
|
258 + getPDGRelease(params.bcs_root_dbdir)
|
|
kkonganti@11
|
259 + '.reference_target.cluster_list.tsv')
|
|
kkonganti@11
|
260 sourmashcompare_mode = 'ani,containment'
|
|
kkonganti@11
|
261 fq_filter_by_len = 0
|
|
kkonganti@11
|
262 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
|
|
kkonganti@11
|
263 fq2_suffix = '_R2_001.fastq.gz'
|
|
kkonganti@11
|
264 }
|
|
kkonganti@11
|
265
|
|
kkonganti@11
|
266 /*
|
|
kkonganti@11
|
267 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
kkonganti@11
|
268 METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
|
|
kkonganti@11
|
269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
kkonganti@11
|
270 */
|
|
kkonganti@11
|
271
|
|
kkonganti@11
|
272 def getPDGRelease(db_path) {
|
|
kkonganti@11
|
273 db_path_obj = new File( db_path )
|
|
kkonganti@11
|
274 def pdg_release = []
|
|
kkonganti@11
|
275
|
|
kkonganti@11
|
276 db_path_obj.eachDirRecurse {
|
|
kkonganti@11
|
277 it.toString() =~ /PDG/ \
|
|
kkonganti@11
|
278 ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
|
|
kkonganti@11
|
279 : null
|
|
kkonganti@11
|
280 }
|
|
kkonganti@11
|
281
|
|
kkonganti@11
|
282 return pdg_release.unique().join('').toString()
|
|
kkonganti@11
|
283 }
|
