Mercurial > repos > galaxytrakr > hfp_nowayout_awsbatch

comparison 0.5.0/workflows/conf/process/nowayout.process.config @ 0:3c767f9cfd88 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:37:56 +0000
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-1:000000000000 0:3c767f9cfd88
1 process {
2 withName: 'SEQKIT_SEQ' {
3 ext.args = [
4 params.fq_filter_by_len ? "-m ${params.fq_filter_by_len}" : ''
5 ].join(' ').trim()
6 }
7
8 // withName: 'SAMTOOLS_FASTQ' {
9 // ext.args = (params.fq_single_end ? '-F 4' : '-f 2')
10 // }
11
12 if (params.fastp_run) {
13 withName: 'FASTP' {
14 ext.args = addParamsToSummary(
15 loadThisFunction("${params.toolshelp}${params.fs}fastp.nf").fastpHelp(params).helpparams
16 )
17 }
18 }
19
20 if (params.kmaalign_run) {
21 withName: 'KMA_ALIGN' {
22 ext.args = addParamsToSummary(
23 loadThisFunction("${params.toolshelp}${params.fs}kmaalign.nf").kmaalignHelp(params).helpparams
24 )
25 }
26 }
27
28 if (params.seqkit_grep_run) {
29 withName: 'SEQKIT_GREP' {
30 ext.args = addParamsToSummary(
31 loadThisFunction("${params.toolshelp}${params.fs}seqkitgrep.nf").seqkitgrepHelp(params).helpparams
32 )
33 }
34 }
35
36 if (params.salmonidx_run){
37 withName: 'SALMON_INDEX' {
38 ext.args = addParamsToSummary(
39 loadThisFunction("${params.toolshelp}${params.fs}salmonidx.nf").salmonidxHelp(params).helpparams
40 )
41 }
42
43 withName: 'SALMON_QUANT' {
44 errorStrategy = 'ignore'
45 ext.args = '--minAssignedFrags 1'
46 }
47 }
48
49 if (params.sourmashsketch_run) {
50 withName: 'SOURMASH_SKETCH' {
51 ext.args = addParamsToSummary(
52 loadThisFunction("${params.toolshelp}${params.fs}sourmashsketch.nf").sourmashsketchHelp(params).helpparams
53 )
54 }
55 }
56
57 if (params.sourmashgather_run) {
58 withName: 'SOURMASH_GATHER' {
59 ext.args = addParamsToSummary(
60 loadThisFunction("${params.toolshelp}${params.fs}sourmashgather.nf").sourmashgatherHelp(params).helpparams
61 )
62
63 if (params.sfhpy_run) {
64 ext.args2 = addParamsToSummary(
65 loadThisFunction("${params.toolshelp}${params.fs}sfhpy.nf").sfhpyHelp(params).helpparams
66 )
67 }
68 }
69 }
70
71 // if (params.sourmashtaxmetagenome_run) {
72 // withName: 'SOURMASH_TAX_METAGENOME' {
73 // ext.args = addParamsToSummary(
74 // loadThisFunction("${params.toolshelp}${params.fs}sourmashtaxmetagenome.nf").sourmashtaxmetagenomeHelp(params).helpparams
75 // )
76 // }
77 // }
78
79 if (params.gsalkronapy_run) {
80 withName: 'NOWAYOUT_RESULTS' {
81 ext.args = addParamsToSummary(
82 loadThisFunction("${params.toolshelp}${params.fs}gsalkronapy.nf").gsalkronapyHelp(params).helpparams
83 )
84 }
85 }
86
87 if (params.krona_ktIT_run) {
88 withName: 'KRONA_KTIMPORTTEXT' {
89 ext.args = addParamsToSummary(
90 loadThisFunction("${params.toolshelp}${params.fs}kronaktimporttext.nf").kronaktimporttextHelp(params).helpparams
91 )
92 }
93 }
94 }
95
96 // Method to instantiate a new function parser
97 // Need to refactor using ScriptParser... another day
98 def loadThisFunction (func_file) {
99 GroovyShell grvy_sh = new GroovyShell()
100 def func = grvy_sh.parse(new File ( func_file ) )
101 return func
102 }
103
104 // Method to add relevant final parameters to summary log
105 def addParamsToSummary(Map params_to_add = [:]) {
106
107 if (!params_to_add.isEmpty()) {
108 def not_null_params_to_add = params_to_add.findAll {
109 it.value.clivalue != null &&
110 it.value.clivalue != '[:]' &&
111 it.value.clivalue != ''
112 }
113
114 params.logtheseparams += not_null_params_to_add.keySet().toList()
115
116 return not_null_params_to_add.collect {
117 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
118 }.join(' ').trim()
119 }
120 return 1
121 }