Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/workflows/bettercallsal_db.nf @ 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 // Define any required imports for this specific workflow
2 import java.nio.file.Paths
3 import nextflow.file.FileHelper
4
5
6 // Include any necessary methods
7 include { \
8 fastqEntryPointHelp; summaryOfParams; stopNow; sendMail; \
9 addPadding; wrapUpHelp } from "${params.routines}"
10 include { wcompHelp } from "${params.toolshelp}${params.fs}wcomp"
11 include { wsnpHelp } from "${params.toolshelp}${params.fs}wsnp"
12 include { mashsketchHelp } from "${params.toolshelp}${params.fs}mashsketch"
13
14
15 // Exit if help requested before any subworkflows
16 if (params.help) {
17 log.info help()
18 exit 0
19 }
20
21
22 // Include any necessary modules and subworkflows
23 include { DOWNLOAD_PDG_METADATA } from "${params.modules}${params.fs}download_pdg_metadata${params.fs}main"
24 include { FILTER_PDG_METADATA } from "${params.modules}${params.fs}filter_pdg_metadata${params.fs}main"
25 include { DB_PER_COMPUTED_SEROTYPE } from "${params.modules}${params.fs}db_per_computed_serotype${params.fs}main"
26 include { DB_PER_SNP_CLUSTER } from "${params.modules}${params.fs}db_per_snp_cluster${params.fs}main"
27 include { INDEX_METADATA } from "${params.modules}${params.fs}index_metadata${params.fs}main"
28 include { SCAFFOLD_GENOMES } from "${params.modules}${params.fs}scaffold_genomes${params.fs}main"
29 include { MASH_SKETCH } from "${params.modules}${params.fs}mash${params.fs}sketch${params.fs}main"
30 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
31
32 /*
33 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
34 INPUTS AND ANY CHECKS FOR THE BETTERCALLSAL_DB WORKFLOW
35 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
36 */
37
38 if (!params.output) {
39 stopNow("Please mention the absolute UNIX path to store the DB flat files\n" +
40 "using the --output option.\n" +
41 "Ex: --output /path/to/bettercallsal/db_files")
42 }
43
44 /*
45 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
46 RUN THE BETTERCALLSAL_DB WORKFLOW
47 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
48 */
49
50 workflow BETTERCALLSAL_DB {
51 main:
52 log.info summaryOfParams()
53
54 DOWNLOAD_PDG_METADATA ( params.pdg_release ?: null )
55
56 DOWNLOAD_PDG_METADATA
57 .out
58 .versions
59 .set { software_versions }
60
61 FILTER_PDG_METADATA (
62 DOWNLOAD_PDG_METADATA.out.accs
63 .splitText(by: params.genomes_chunk.toInteger() * 10, file: true)
64 )
65
66 DB_PER_COMPUTED_SEROTYPE (
67 FILTER_PDG_METADATA.out.accs_chunk_tbl
68 .collectFile(name: 'per_comp_db_accs.txt'),
69 DOWNLOAD_PDG_METADATA.out.pdg_metadata
70 )
71
72 DB_PER_SNP_CLUSTER (
73 FILTER_PDG_METADATA.out.accs_chunk_tbl
74 .collectFile(name: 'per_snp_db_accs.txt'),
75 DOWNLOAD_PDG_METADATA.out.pdg_metadata,
76 DOWNLOAD_PDG_METADATA.out.snp_cluster_metadata
77 )
78
79 DB_PER_COMPUTED_SEROTYPE.out.genome_paths
80 .map { query ->
81 kv = [:]
82 kv['id'] = 'comp'
83 [ kv, query ]
84 }
85 .concat(
86 DB_PER_SNP_CLUSTER.out.genome_paths
87 .map { query ->
88 kv = [:]
89 kv['id'] = 'snp'
90 [ kv, query ]
91 }
92 )
93 .groupTuple(by: [0])
94 .set { ch_mash_these_genomes }
95
96 DB_PER_SNP_CLUSTER
97 .out
98 .asm_chunk_snp_tbl
99 .concat( DB_PER_COMPUTED_SEROTYPE.out.asm_chunk_comp_tbl )
100 .map { acc -> [ acc.name.find(/\_comp|\_snp/), acc ] }
101 .set { ch_index_metadata }
102
103 INDEX_METADATA ( ch_index_metadata )
104
105 DB_PER_COMPUTED_SEROTYPE.out.accs_comp
106 .concat( DB_PER_SNP_CLUSTER.out.accs_snp )
107 .splitText()
108 .collect()
109 .flatten()
110 .unique()
111 .collectFile(name: 'accs_to_download.txt')
112 .splitText(by: params.genomes_chunk, file: true)
113 .set { ch_accs_to_download }
114
115 SCAFFOLD_GENOMES ( ch_accs_to_download )
116
117 SCAFFOLD_GENOMES
118 .out
119 .genomes_dir
120 .toSortedList()
121 .flatten()
122 .unique()
123 .set { ch_genomes_dir }
124
125 MASH_SKETCH (
126 ch_mash_these_genomes.combine( ch_genomes_dir )
127 )
128
129 DUMP_SOFTWARE_VERSIONS (
130 software_versions
131 .mix (
132 DOWNLOAD_PDG_METADATA.out.versions,
133 FILTER_PDG_METADATA.out.versions,
134 DB_PER_COMPUTED_SEROTYPE.out.versions,
135 DB_PER_SNP_CLUSTER.out.versions,
136 INDEX_METADATA.out.versions,
137 SCAFFOLD_GENOMES.out.versions,
138 MASH_SKETCH.out.versions,
139 )
140 .unique()
141 .collectFile(name: 'collected_versions.yml')
142 )
143 }
144
145 /*
146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
147 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 */
150
151 workflow.onComplete {
152 if (workflow.success) {
153 sendMail()
154 }
155 }
156
157 workflow.onError {
158 sendMail()
159 }
160
161 /*
162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
163 HELP TEXT METHODS FOR BETTERCALLSAL_DB WORKFLOW
164 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
165 */
166
167 def help() {
168
169 Map helptext = [:]
170
171 helptext.putAll (
172 fastqEntryPointHelp().findAll {
173 it.key =~ /Required|output|Other|Workflow|Author|Version/
174 } +
175 wcompHelp(params).text +
176 wsnpHelp(params).text +
177 mashsketchHelp(params).text +
178 wrapUpHelp()
179 )
180
181 return addPadding(helptext)
182 }