Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.3.0/workflows/conf/process/centriflaken_hy.process.config @ 92:295c2597a475

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:07:24 -0400
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91:046e57368d3b 92:295c2597a475
1 process {
2 withName: 'SEQKIT_SEQ' {
3 ext.args = [
4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
5 ].join(' ').trim()
6 }
7
8 if (params.seqkit_grep_on) {
9 withName: 'SEQKIT_GREP' {
10 ext.args = addParamsToSummary(
11 loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
12 )
13 }
14 }
15
16 withName: 'CENTRIFUGE_CLASSIFY' {
17 ext.args = addParamsToSummary(
18 loadThisFunction("${params.toolshelp}${params.fs}centrifuge.nf").centrifugeHelp(params).helpparams
19 )
20 }
21
22 withName: 'KRAKEN2_CLASSIFY' {
23 ext.args = addParamsToSummary(
24 loadThisFunction("${params.toolshelp}${params.fs}kraken2.nf").kraken2Help(params).helpparams
25 )
26 }
27
28 withName: 'MEGAHIT_ASSEMBLE' {
29 ext.when = params.megahit_run
30 errorStrategy = 'ignore'
31 ext.args = addParamsToSummary(
32 loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
33 )
34 }
35
36 withName: 'SPADES_ASSEMBLE' {
37 ext.when = params.spades_run
38 errorStrategy = 'ignore'
39 ext.args = addParamsToSummary(
40 loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
41 )
42 }
43
44 if (params.ectyper_run) {
45 withName: 'ECTYPER' {
46 ext.when = params.ectyper_run
47 ext.args = addParamsToSummary(
48 loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams
49 )
50 }
51 }
52
53 withName: 'SEROTYPEFINDER' {
54 ext.when = params.serotypefinder_run
55 ext.args = addParamsToSummary(
56 loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams
57 )
58 }
59
60 withName: 'SEQSERO2' {
61 ext.when = params.seqsero2_run
62 ext.args = addParamsToSummary(
63 loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams
64 )
65 }
66
67 withName: 'MLST' {
68 ext.when = params.mlst_run
69 ext.args = addParamsToSummary(
70 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
71 )
72 }
73
74 if (params.amrfinderplus_run) {
75 withName: 'AMRFINDERPLUS_RUN' {
76 ext.when = params.amrfinderplus_run
77 ext.args = addParamsToSummary(
78 loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams
79 )
80 }
81 }
82
83 withName: 'ABRICATE_RUN' {
84 ext.when = params.abricate_run
85 ext.args = addParamsToSummary(
86 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
87 )
88 }
89
90 withName: 'ABRICATE_SUMMARY' {
91 ext.when = params.abricate_summary_run
92 }
93 }
94
95 // Method to instantiate a new function parser
96 // Need to refactor using ScriptParser... another day
97 def loadThisFunction (func_file) {
98 GroovyShell grvy_sh = new GroovyShell()
99 def func = grvy_sh.parse(new File ( func_file ) )
100 return func
101 }
102
103 // Method to add relevant final parameters to summary log
104 def addParamsToSummary(Map params_to_add = [:]) {
105
106 if (!params_to_add.isEmpty()) {
107 def not_null_params_to_add = params_to_add.findAll {
108 it.value.clivalue != null &&
109 it.value.clivalue != '[:]' &&
110 it.value.clivalue != ''
111 }
112
113 params.logtheseparams += not_null_params_to_add.keySet().toList()
114
115 return not_null_params_to_add.collect {
116 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
117 }.join(' ').trim()
118 }
119 return 1
120 }