Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/workflows/conf/process/bettercallsal.process.config @ 0:0a8dda29956e draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 process {
2 withName: 'SEQKIT_SEQ' {
3 ext.args = [
4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
5 ].join(' ').trim()
6 }
7
8 if (params.bbmerge_run) {
9 withName: 'BBTOOLS_BBMERGE' {
10 ext.args = addParamsToSummary(
11 loadThisFunction("${params.toolshelp}${params.fs}bbmerge.nf").bbmergeHelp(params).helpparams
12 )
13 }
14 }
15
16 if (params.fastp_run) {
17 withName: 'FASTP' {
18 ext.args = addParamsToSummary(
19 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
20 )
21 }
22 }
23
24 if (params.bcs_concat_pe) {
25 withName: 'CAT_CAT' {
26 ext.prefix = 'concat.fastq.gz'
27 }
28 }
29
30
31 if (params.mashscreen_run) {
32 withName: 'MASH_SCREEN' {
33 ext.args = addParamsToSummary(
34 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
35 )
36 }
37 }
38
39 if (params.tuspy_run) {
40 withName: 'TOP_UNIQUE_SEROVARS' {
41 ext.args = addParamsToSummary(
42 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
43 )
44 }
45 }
46
47 if (params.gsrpy_run) {
48 withName: 'BCS_RESULTS' {
49 ext.args = addParamsToSummary(
50 loadThisFunction("${params.toolshelp}${params.fs}gsrpy.nf").gsrpyHelp(params).helpparams
51 )
52 }
53 }
54
55 if (params.sourmashsketch_run) {
56 withName: 'SOURMASH_SKETCH' {
57 ext.args = addParamsToSummary(
58 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
59 )
60 }
61 }
62
63 if (params.sourmashgather_run) {
64 withName: 'SOURMASH_GATHER' {
65 ext.args = addParamsToSummary(
66 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
67 )
68
69 if (params.sfhpy_run) {
70 ext.args2 = addParamsToSummary(
71 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
72 )
73 }
74 }
75 }
76
77 if (params.sourmashsearch_run) {
78 withName: 'SOURMASH_SEARCH' {
79 ext.args = addParamsToSummary(
80 loadThisFunction("${params.toolshelp}${params.fs}sourmashsearch.nf").sourmashsearchHelp(params).helpparams
81 )
82
83 if (params.sfhpy_run) {
84 ext.args2 = addParamsToSummary(
85 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
86 )
87 }
88 }
89 }
90
91 if (params.kmaindex_run) {
92 withName: 'KMA_INDEX' {
93 ext.args = addParamsToSummary(
94 loadThisFunction("${params.toolshelp}${params.fs}kmaindex.nf").kmaindexHelp(params).helpparams
95 )
96 }
97 }
98
99 if (params.kmaalign_run) {
100 withName: 'KMA_ALIGN' {
101 ext.args = addParamsToSummary(
102 loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
103 )
104 }
105 }
106
107 if (params.megahit_run) {
108 withName: 'MEGAHIT_ASSEMBLE' {
109 errorStrategy = 'ignore'
110 ext.args = addParamsToSummary(
111 loadThisFunction("${params.toolshelp}${params.fs}megahit.nf").megahitHelp(params).helpparams
112 )
113 }
114
115 withName: 'MLST' {
116 ext.when = params.mlst_run
117 ext.args = addParamsToSummary(
118 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
119 )
120 }
121
122 withName: 'ABRICATE_RUN' {
123 ext.when = params.abricate_run
124 ext.args = addParamsToSummary(
125 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
126 )
127 }
128
129 withName: 'ABRICATE_SUMMARY' {
130 ext.when = params.abricate_summary_run
131 }
132 }
133
134 if (params.salmonidx_run) {
135 withName: 'SALMON_INDEX' {
136 ext.args = addParamsToSummary(
137 loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
138 )
139 }
140 }
141
142 withName: 'OTF_GENOME' {
143 errorStrategy = 'ignore'
144 }
145
146 }
147
148
149 // Parse the default params
150 def loadThisFunction (func_file) {
151 GroovyShell grvy_sh = new GroovyShell()
152 def func = grvy_sh.parse(new File ( func_file ) )
153 return func
154 }
155
156 // Method to add relevant final parameters to summary log
157 def addParamsToSummary(Map params_to_add = [:]) {
158
159 if (!params_to_add.isEmpty()) {
160 def not_null_params_to_add = params_to_add.findAll {
161 it.value.clivalue != null &&
162 it.value.clivalue != '[:]' &&
163 it.value.clivalue != ''
164 }
165
166 params.logtheseparams += not_null_params_to_add.keySet().toList()
167
168 return not_null_params_to_add.collect {
169 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
170 }.join(' ').trim()
171 }
172 return 1
173 }