Mercurial > repos > galaxytrakr > hfp_cronology_awsbatch

comparison 0.2.0/workflows/conf/process/cronology.process.config @ 0:9e8b1c747a6a draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 process {
2 withName: 'SEQKIT_SEQ' {
3 ext.args = [
4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
5 ].join(' ').trim()
6 }
7
8 if (params.dpubmlstpy_run) {
9 withName: 'DOWNLOAD_PUBMLST_SCHEME' {
10 ext.args = addParamsToSummary(
11 loadThisFunction("${params.toolshelp}${params.fs}dpubmlstpy.nf").dpubmlstpyHelp(params).helpparams
12 )
13 }
14 }
15
16 if (params.fastp_run) {
17 withName: 'FASTP' {
18 ext.args = addParamsToSummary(
19 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
20 )
21 }
22 }
23
24 if (params.mashscreen_run) {
25 withName: 'MASH_SCREEN' {
26 ext.args = addParamsToSummary(
27 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
28 )
29 }
30 }
31
32 if (params.tuspy_run) {
33 withName: 'TOP_UNIQUE_SEROVARS' {
34 ext.args = addParamsToSummary(
35 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
36 )
37 }
38 }
39
40 if (params.spades_run) {
41 withName: 'SPADES_ASSEMBLE' {
42 errorStrategy = 'ignore'
43 ext.args = addParamsToSummary(
44 loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
45 )
46 }
47 }
48
49 if (params.shovill_run) {
50 withName: 'SHOVILL' {
51 errorStrategy = 'ignore'
52 ext.args = addParamsToSummary(
53 loadThisFunction("${params.toolshelp}${params.fs}shovill.nf").shovillHelp(params).helpparams
54 )
55 }
56 }
57
58 if (params.polypolish_run) {
59 withName: 'POLYPOLISH' {
60 ext.args = addParamsToSummary(
61 loadThisFunction("${params.toolshelp}${params.fs}polypolish.nf").polypolishHelp(params).helpparams
62 )
63 }
64 }
65
66 if (params.quast_run) {
67 withName: 'QUAST' {
68 ext.args = addParamsToSummary(
69 loadThisFunction("${params.toolshelp}${params.fs}quast.nf").quastHelp(params).helpparams
70 )
71 }
72 }
73
74 if (params.pirate_run) {
75 withName: 'PIRATE' {
76 ext.args = addParamsToSummary(
77 loadThisFunction("${params.toolshelp}${params.fs}pirate.nf").pirateHelp(params).helpparams
78 )
79 }
80 }
81
82 if (params.prodka_run) {
83 withName: 'PRODIGAL' {
84 ext.args = addParamsToSummary(
85 loadThisFunction("${params.toolshelp}${params.fs}prodigal.nf").prodigalHelp(params).helpparams
86 )
87 }
88
89 withName: 'PROKKA' {
90 ext.args = addParamsToSummary(
91 loadThisFunction("${params.toolshelp}${params.fs}prokka.nf").prokkaHelp(params).helpparams
92 )
93 }
94 }
95
96 if (params.mlst_run) {
97 withName: 'MLST' {
98 ext.args = addParamsToSummary(
99 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
100 )
101 }
102 }
103
104 if (params.abricate_run) {
105 withName: 'ABRICATE_RUN' {
106 ext.args = addParamsToSummary(
107 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
108 )
109 }
110 }
111
112 if (params.mashtree_run) {
113 withName: 'MASHTREE' {
114 ext.args = addParamsToSummary(
115 loadThisFunction("${params.toolshelp}${params.fs}mashtree.nf").mashtreeHelp(params).helpparams
116 )
117 }
118 }
119
120 if (params.upload_microreact) {
121 withName: 'UPLOAD_MICROREACT' {
122 errorStrategy = 'ignore'
123 }
124 }
125 }
126
127 // Method to instantiate a new function parser
128 // Need to refactor using ScriptParser... another day
129 def loadThisFunction (func_file) {
130 GroovyShell grvy_sh = new GroovyShell()
131 def func = grvy_sh.parse(new File ( func_file ) )
132 return func
133 }
134
135 // Method to add relevant final parameters to summary log
136 def addParamsToSummary(Map params_to_add = [:]) {
137
138 if (!params_to_add.isEmpty()) {
139 def not_null_params_to_add = params_to_add.findAll {
140 it.value.clivalue != null &&
141 it.value.clivalue != '[:]' &&
142 it.value.clivalue != ''
143 }
144
145 params.logtheseparams += not_null_params_to_add.keySet().toList()
146
147 return not_null_params_to_add.collect {
148 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
149 }.join(' ').trim()
150 }
151 return 1
152 }