Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/workflows/conf/process/bettercallsal_lr.process.config @ 0:801b85b03a17 draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 process {
2 withName: 'SEQKIT_SEQ' {
3 ext.args = [
4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
5 ].join(' ').trim()
6 }
7
8 if (params.filtlong_run) {
9 withName: 'FILTLONG' {
10 ext.args = addParamsToSummary(
11 loadThisFunction("${params.toolshelp}${params.fs}filtlong.nf").filtlongHelp(params).helpparams
12 )
13 }
14 }
15
16 if (params.mashscreen_run) {
17 withName: 'MASH_SCREEN' {
18 ext.args = addParamsToSummary(
19 loadThisFunction("${params.toolshelp}${params.fs}mashscreen.nf").mashscreenHelp(params).helpparams
20 )
21 }
22 }
23
24 if (params.tuspy_run) {
25 withName: 'TOP_UNIQUE_SEROVARS' {
26 ext.args = addParamsToSummary(
27 loadThisFunction("${params.toolshelp}${params.fs}tuspy.nf").tuspyHelp(params).helpparams
28 )
29 }
30 }
31
32 if (params.gsrpy_run) {
33 withName: 'BCS_RESULTS' {
34 ext.args = addParamsToSummary(
35 loadThisFunction("${params.toolshelp}${params.fs}gsrpy.nf").gsrpyHelp(params).helpparams
36 )
37 }
38 }
39
40 if (params.sourmashsketch_run) {
41 withName: 'SOURMASH_SKETCH' {
42 ext.args = addParamsToSummary(
43 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
44 )
45 }
46 }
47
48 if (params.sourmashgather_run) {
49 withName: 'SOURMASH_GATHER' {
50 ext.args = addParamsToSummary(
51 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
52 )
53
54 if (params.sfhpy_run) {
55 ext.args2 = addParamsToSummary(
56 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
57 )
58 }
59 }
60 }
61
62 if (params.sourmashsearch_run) {
63 withName: 'SOURMASH_SEARCH' {
64 ext.args = addParamsToSummary(
65 loadThisFunction("${params.toolshelp}${params.fs}sourmashsearch.nf").sourmashsearchHelp(params).helpparams
66 )
67
68 if (params.sfhpy_run) {
69 ext.args2 = addParamsToSummary(
70 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
71 )
72 }
73 }
74 }
75
76 if (params.flye_run) {
77 withName: 'FLYE_ASSEMBLE' {
78 errorStrategy = 'ignore'
79 ext.args = addParamsToSummary(
80 loadThisFunction("${params.toolshelp}${params.fs}flye.nf").flyeHelp(params).helpparams
81 )
82 }
83
84 withName: 'MINIMAP2_ALIGN' {
85 ext.args = '-ax map-ont'
86 }
87
88 withName: 'MLST' {
89 ext.when = params.mlst_run
90 ext.args = addParamsToSummary(
91 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
92 )
93 }
94
95 withName: 'ABRICATE_RUN' {
96 ext.when = params.abricate_run
97 ext.args = addParamsToSummary(
98 loadThisFunction("${params.toolshelp}${params.fs}abricate.nf").abricateHelp(params).helpparams
99 )
100 }
101
102 withName: 'ABRICATE_SUMMARY' {
103 ext.when = params.abricate_summary_run
104 }
105 }
106
107 withName: 'SALMON_QUANT' {
108 ext.args = '--ont'
109 }
110
111 withName: 'OTF_GENOME' {
112 errorStrategy = 'ignore'
113 }
114
115 }
116
117
118 // Parse the default params
119 def loadThisFunction (func_file) {
120 GroovyShell grvy_sh = new GroovyShell()
121 def func = grvy_sh.parse(new File ( func_file ) )
122 return func
123 }
124
125 // Method to add relevant final parameters to summary log
126 def addParamsToSummary(Map params_to_add = [:]) {
127
128 if (!params_to_add.isEmpty()) {
129 def not_null_params_to_add = params_to_add.findAll {
130 it.value.clivalue != null &&
131 it.value.clivalue != '[:]' &&
132 it.value.clivalue != ''
133 }
134
135 params.logtheseparams += not_null_params_to_add.keySet().toList()
136
137 return not_null_params_to_add.collect {
138 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
139 }.join(' ').trim()
140 }
141 return 1
142 }