Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.0/workflows/conf/process/centriflaken.process.config @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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100:9d9537c907bd 101:ce6d9548fe89
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}${params.fs}kraken2.nf").kraken2Help(params).helpparams
25 )
26 }
27
28 withName: 'FLYE_ASSEMBLE' {
29 errorStrategy = 'ignore'
30 ext.args = addParamsToSummary(
31 loadThisFunction("${params.toolshelp}${params.fs}flye.nf").flyeHelp(params).helpparams
32 )
33 }
34
35 if (params.ectyper_run) {
36 withName: 'ECTYPER' {
37 ext.when = params.ectyper_run
38 ext.args = addParamsToSummary(
39 loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams
40 )
41 }
42 }
43
44 withName: 'SEROTYPEFINDER' {
45 ext.when = params.serotypefinder_run
46 ext.args = addParamsToSummary(
47 loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams
48 )
49 }
50
51 withName: 'SEQSERO2' {
52 ext.when = params.seqsero2_run
53 ext.args = addParamsToSummary(
54 loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams
55 )
56 }
57
58 withName: 'MLST' {
59 ext.when = params.mlst_run
60 ext.args = addParamsToSummary(
61 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
62 )
63 }
64
65 if (params.amrfinderplus_run) {
66 withName: 'AMRFINDERPLUS_RUN' {
67 ext.when = params.amrfinderplus_run
68 ext.args = addParamsToSummary(
69 loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams
70 )
71 }
72 }
73
74 withName: 'ABRICATE_RUN' {
75 ext.when = params.abricate_run
76 ext.args = addParamsToSummary(
77 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
78 )
79 }
80
81 withName: 'ABRICATE_SUMMARY' {
82 ext.when = params.abricate_summary_run
83 }
84 }
85
86 // Method to instantiate a new function parser
87 // Need to refactor using ScriptParser... another day
88 def loadThisFunction (func_file) {
89 GroovyShell grvy_sh = new GroovyShell()
90 def func = grvy_sh.parse(new File ( func_file ) )
91 return func
92 }
93
94 // Method to add relevant final parameters to summary log
95 def addParamsToSummary(Map params_to_add = [:]) {
96
97 if (!params_to_add.isEmpty()) {
98 def not_null_params_to_add = params_to_add.findAll {
99 it.value.clivalue != null &&
100 it.value.clivalue != '[:]' &&
101 it.value.clivalue != ''
102 }
103
104 params.logtheseparams += not_null_params_to_add.keySet().toList()
105
106 return not_null_params_to_add.collect {
107 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
108 }.join(' ').trim()
109 }
110 return 1
111 }