Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch

comparison 0.4.2/workflows/conf/process/centriflaken_hy.process.config @ 0:082e0091e813 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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-1:000000000000 0:082e0091e813
1 process {
2 withName: 'SEQKIT_SEQ' {
3 ext.args = [
4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
5 ].join(' ').trim()
6 }
7
8 if (params.seqkit_rmdup_run) {
9 withName: 'SEQKIT_RMDUP' {
10 ext.when = params.seqkit_rmdup_run
11 ext.args = addParamsToSummary(
12 loadThisFunction("${params.toolshelp}${params.fs}seqkitrmdup.nf").seqkitrmdupHelp(params).helpparams
13 )
14 }
15 }
16
17 if (params.seqkit_grep_on) {
18 withName: 'SEQKIT_GREP' {
19 ext.args = addParamsToSummary(
20 loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
21 )
22 }
23 }
24
25 withName: 'CENTRIFUGE_CLASSIFY' {
26 ext.args = addParamsToSummary(
27 loadThisFunction("${params.toolshelp}${params.fs}centrifuge.nf").centrifugeHelp(params).helpparams
28 )
29 }
30
31 withName: 'KRAKEN2_CLASSIFY' {
32 ext.args = addParamsToSummary(
33 loadThisFunction("${params.toolshelp}${params.fs}kraken2.nf").kraken2Help(params).helpparams
34 )
35 }
36
37 withName: 'MEGAHIT_ASSEMBLE' {
38 ext.when = params.megahit_run
39 errorStrategy = 'ignore'
40 ext.args = addParamsToSummary(
41 loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
42 )
43 }
44
45 withName: 'SPADES_ASSEMBLE' {
46 ext.when = params.spades_run
47 errorStrategy = 'ignore'
48 ext.args = addParamsToSummary(
49 loadThisFunction("${params.toolshelp}${params.fs}spades.nf").spadesHelp(params).helpparams
50 )
51 }
52
53 if (params.ectyper_run) {
54 withName: 'ECTYPER' {
55 ext.when = params.ectyper_run
56 ext.args = addParamsToSummary(
57 loadThisFunction("${params.toolshelp}${params.fs}ectyper.nf").ectyperHelp(params).helpparams
58 )
59 }
60 }
61
62 withName: 'SEROTYPEFINDER' {
63 ext.when = params.serotypefinder_run
64 ext.args = addParamsToSummary(
65 loadThisFunction("${params.toolshelp}${params.fs}serotypefinder.nf").serotypefinderHelp(params).helpparams
66 )
67 }
68
69 withName: 'SEQSERO2' {
70 ext.when = params.seqsero2_run
71 ext.args = addParamsToSummary(
72 loadThisFunction("${params.toolshelp}${params.fs}seqsero2.nf").seqsero2Help(params).helpparams
73 )
74 }
75
76 withName: 'MLST' {
77 ext.when = params.mlst_run
78 ext.args = addParamsToSummary(
79 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
80 )
81 }
82
83 if (params.amrfinderplus_run) {
84 withName: 'AMRFINDERPLUS_RUN' {
85 ext.when = params.amrfinderplus_run
86 ext.args = addParamsToSummary(
87 loadThisFunction("${params.toolshelp}${params.fs}amrfinderplus.nf").amrfinderplusHelp(params).helpparams
88 )
89 }
90 }
91
92 withName: 'ABRICATE_RUN' {
93 ext.when = params.abricate_run
94 ext.args = addParamsToSummary(
95 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
96 )
97 }
98
99 withName: 'ABRICATE_SUMMARY' {
100 ext.when = params.abricate_summary_run
101 }
102 }
103
104 // Method to instantiate a new function parser
105 // Need to refactor using ScriptParser... another day
106 def loadThisFunction (func_file) {
107 GroovyShell grvy_sh = new GroovyShell()
108 def func = grvy_sh.parse(new File ( func_file ) )
109 return func
110 }
111
112 // Method to add relevant final parameters to summary log
113 def addParamsToSummary(Map params_to_add = [:]) {
114
115 if (!params_to_add.isEmpty()) {
116 def not_null_params_to_add = params_to_add.findAll {
117 it.value.clivalue != null &&
118 it.value.clivalue != '[:]' &&
119 it.value.clivalue != ''
120 }
121
122 params.logtheseparams += not_null_params_to_add.keySet().toList()
123
124 return not_null_params_to_add.collect {
125 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
126 }.join(' ').trim()
127 }
128 return 1
129 }