Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.5.0/workflows/bettercallsal_db.nf @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
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 ( DOWNLOAD_PDG_METADATA.out.accs )
62
63 DB_PER_COMPUTED_SEROTYPE (
64 FILTER_PDG_METADATA.out.accs_chunk_tbl,
65 DOWNLOAD_PDG_METADATA.out.pdg_metadata
66 )
67
68 DB_PER_SNP_CLUSTER (
69 FILTER_PDG_METADATA.out.accs_chunk_tbl,
70 DOWNLOAD_PDG_METADATA.out.pdg_metadata,
71 DOWNLOAD_PDG_METADATA.out.snp_cluster_metadata
72 )
73
74 DB_PER_COMPUTED_SEROTYPE.out.genome_paths
75 .map { query ->
76 kv = [:]
77 kv['id'] = 'comp'
78 [ kv, query ]
79 }
80 .concat(
81 DB_PER_SNP_CLUSTER.out.genome_paths
82 .map { query ->
83 kv = [:]
84 kv['id'] = 'snp'
85 [ kv, query ]
86 }
87 )
88 .groupTuple(by: [0])
89 .set { ch_mash_these_genomes }
90
91 DB_PER_SNP_CLUSTER
92 .out
93 .asm_chunk_snp_tbl
94 .concat( DB_PER_COMPUTED_SEROTYPE.out.asm_chunk_comp_tbl )
95 .map { acc ->
96 [ acc.name.find(/\_comp|\_snp/), acc ]
97 }
98 .set { ch_index_metadata }
99
100 INDEX_METADATA ( ch_index_metadata )
101
102 DB_PER_COMPUTED_SEROTYPE.out.accs_comp
103 .concat( DB_PER_SNP_CLUSTER.out.accs_snp )
104 .collectFile(name: 'accs_to_download.txt')
105 .splitText(by: params.genomes_chunk, file: true)
106 .set { ch_accs_to_download }
107
108 SCAFFOLD_GENOMES ( ch_accs_to_download )
109
110 SCAFFOLD_GENOMES
111 .out
112 .genomes_dir
113 .toSortedList()
114 .flatten()
115 .unique()
116 .set { ch_genomes_dir }
117
118 MASH_SKETCH (
119 ch_mash_these_genomes.combine( ch_genomes_dir )
120 )
121
122 DUMP_SOFTWARE_VERSIONS (
123 software_versions
124 .mix (
125 DOWNLOAD_PDG_METADATA.out.versions,
126 FILTER_PDG_METADATA.out.versions,
127 DB_PER_COMPUTED_SEROTYPE.out.versions,
128 DB_PER_SNP_CLUSTER.out.versions,
129 INDEX_METADATA.out.versions,
130 SCAFFOLD_GENOMES.out.versions,
131 MASH_SKETCH.out.versions,
132 )
133 .unique()
134 .collectFile(name: 'collected_versions.yml')
135 )
136 }
137
138 /*
139 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
140 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
141 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
142 */
143
144 workflow.onComplete {
145 if (workflow.success) {
146 sendMail()
147 }
148 }
149
150 workflow.onError {
151 sendMail()
152 }
153
154 /*
155 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
156 HELP TEXT METHODS FOR BETTERCALLSAL_DB WORKFLOW
157 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
158 */
159
160 def help() {
161
162 Map helptext = [:]
163
164 helptext.putAll (
165 fastqEntryPointHelp().findAll {
166 it.key =~ /Required|output|Other|Workflow|Author|Version/
167 } +
168 wcompHelp(params).text +
169 wsnpHelp(params).text +
170 mashsketchHelp(params).text +
171 wrapUpHelp()
172 )
173
174 return addPadding(helptext)
175 }