Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/workflows/conf/bettercallsal_lr.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 filtlong_run = true
10 filtlong_keep_perc = false
11 filtlong_target_bases = false
12 filtlong_min_length = 1000
13 filtlong_max_length = 20000
14 filtlong_min_mean_q = 75
15 filtlong_min_window_q = 75
16 filtlong_a = false
17 filtlong_1 = false
18 filtlong_2 = false
19 filtlong_len_weight = false
20 filtlong_mean_q_weight = 30
21 filtlong_window_q_weight = 30
22 filtlong_trim = false
23 filtlong_split = false
24 filtlong_window_size = 250
25 mashscreen_run = true
26 mash_sketch = (params.bcs_root_dbdir
27 + File.separator
28 + 'mash_sketch'
29 + File.separator
30 + 'msh.k21.1000h.'
31 + params.bcs_db_mode
32 + '.msh')
33 mashscreen_w = false
34 mashscreen_i = false
35 mashscreen_v = false
36 tuspy_run = true
37 tuspy_s = false
38 tuspy_m = false
39 tuspy_ps = (params.bcs_root_dbdir
40 + File.separator
41 + 'index_metadata'
42 + File.separator
43 + 'per_'
44 + params.bcs_db_mode
45 + params.bcs_db_mode_index
46 + '.ACC2SERO.pickle')
47 tuspy_gd = (params.bcs_root_dbdir
48 + File.separator
49 + 'scaffold_genomes')
50 tuspy_gds = '_scaffolded_genomic.fna.gz'
51 tuspy_n = 10
52 tuspy_skip = 'PRJNA766315,PRJNA675435,PRJNA831577,PRJNA855361'
53 sourmashsketch_run = true
54 sourmashsketch_mode = 'dna'
55 sourmashsketch_file = false
56 sourmashsketch_f = false
57 sourmashsketch_merge = false
58 sourmashsketch_name = false
59 sourmashsketch_p = 'abund,scaled=1000,k=51,k=61,k=71,k=81,k=91,k=101'
60 sourmashsketch_singleton = true
61 sourmashsketch_randomize = false
62 sourmashgather_run = (params.sourmashsketch_run ?: false)
63 sourmashgather_n = false
64 sourmashgather_thr_bp = false
65 sourmashgather_ignoreabn = false
66 sourmashgather_prefetch = false
67 sourmashgather_noprefetch = false
68 sourmashgather_ani_ci = true
69 sourmashgather_k = 81
70 sourmashgather_protein = false
71 sourmashgather_noprotein = false
72 sourmashgather_dayhoff = false
73 sourmashgather_nodayhoff = false
74 sourmashgather_hp = false
75 sourmashgather_nohp = false
76 sourmashgather_dna = true
77 sourmashgather_nodna = false
78 sourmashgather_scaled = false
79 sourmashgather_inc_pat = false
80 sourmashgather_exc_pat = false
81 sourmashsearch_run = (params.sourmashsketch_run && !params.sourmashgather_run ?: false)
82 sourmashsearch_n = false
83 sourmashsearch_thr = '0'
84 sourmashsearch_contain = false
85 sourmashsearch_maxcontain = true
86 sourmashsearch_ignoreabn = true
87 sourmashsearch_ani_ci = false
88 sourmashsearch_k = 81
89 sourmashsearch_protein = false
90 sourmashsearch_noprotein = false
91 sourmashsearch_dayhoff = false
92 sourmashsearch_nodayhoff = false
93 sourmashsearch_hp = false
94 sourmashsearch_nohp = false
95 sourmashsearch_dna = true
96 sourmashsearch_nodna = false
97 sourmashsearch_scaled = false
98 sourmashsearch_inc_pat = false
99 sourmashsearch_exc_pat = false
100 sfhpy_run = true
101 sfhpy_fcn = (params.sourmashsearch_run ? 'similarity' : 'f_match')
102 sfhpy_fcv = (params.sourmashsearch_run ? 0.9 : 0.05)
103 sfhpy_gt = true
104 sfhpy_lt = false
105 salmonalign_libtype = 'U'
106 flye_run = true
107 flye_pacbio_raw = false
108 flye_pacbio_corr = false
109 flye_pacbio_hifi = false
110 flye_nano_raw = false
111 flye_nano_corr = true
112 flye_nano_hq = false
113 flye_genome_size = false
114 flye_polish_iter = '3'
115 flye_min_overlap = false
116 flye_scaffold = false
117 flye_meta = true
118 mm2_align_bam = true
119 mm2_align_bam_sorted = false
120 mm2_align_cigar_paf = false
121 mm2_align_cigar_bam = false
122 mlst_run = true
123 mlst_scheme = 'senterica_achtman_2'
124 mlst_legacy = true
125 mlst_minid = 95
126 mlst_mincov = 10
127 mlst_minscore = 50
128 abricate_run = true
129 abricate_datadir = ("${projectDir}"
130 + File.separator
131 + 'assets'
132 + File.separator
133 + 'abricate_dbs')
134 abricate_minid = 90
135 abricate_mincov = 80
136 abricate_summary_run = true
137 gsrpy_run = true
138 gsrpy_url = true
139 gsrpy_snp_clus_metadata = (params.bcs_root_dbdir
140 + File.separator
141 + 'download_pdg_metadata'
142 + File.separator
143 + getPDGRelease(params.bcs_root_dbdir)
144 + File.separator
145 + getPDGRelease(params.bcs_root_dbdir)
146 + '.reference_target.cluster_list.tsv')
147 sourmashcompare_mode = 'ani,containment'
148 fq_filter_by_len = 0
149 fq_filename_delim_idx = 3
150 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
151 fq2_suffix = '_R2_001.fastq.gz'
152 multiqc_run = true
153 }
154
155 /*
156 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
157 METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
158 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
159 */
160
161 def getPDGRelease(db_path) {
162 db_path_obj = new File( db_path )
163 def pdg_release = []
164
165 db_path_obj.eachDirRecurse {
166 it.toString() =~ /PDG/ \
167 ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
168 : null
169 }
170
171 return pdg_release.unique().join('').toString()
172 }