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kkonganti@0
|
1 process {
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kkonganti@0
|
2 if (params.dpubmlstpy_run) {
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kkonganti@0
|
3 withName: 'DOWNLOAD_PUBMLST_SCHEME' {
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kkonganti@0
|
4 ext.args = addParamsToSummary(
|
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kkonganti@0
|
5 loadThisFunction("${params.toolshelp}${params.fs}dpubmlstpy.nf").dpubmlstpyHelp(params).helpparams
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kkonganti@0
|
6 )
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|
kkonganti@0
|
7 }
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|
kkonganti@0
|
8 }
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|
kkonganti@0
|
9
|
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kkonganti@0
|
10 if (params.checkm2predict_run) {
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|
kkonganti@0
|
11 withName: 'CHECKM2_PREDICT' {
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|
kkonganti@0
|
12 ext.args = addParamsToSummary(
|
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kkonganti@0
|
13 loadThisFunction("${params.toolshelp}${params.fs}checkm2predict.nf").checkm2predictHelp(params).helpparams
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|
kkonganti@0
|
14 )
|
|
kkonganti@0
|
15 }
|
|
kkonganti@0
|
16 }
|
|
kkonganti@0
|
17
|
|
kkonganti@0
|
18 if (params.guncrun_run) {
|
|
kkonganti@0
|
19 withName: 'GUNC_RUN' {
|
|
kkonganti@0
|
20 ext.args = addParamsToSummary(
|
|
kkonganti@0
|
21 loadThisFunction("${params.toolshelp}${params.fs}guncrun.nf").guncrunHelp(params).helpparams
|
|
kkonganti@0
|
22 )
|
|
kkonganti@0
|
23 }
|
|
kkonganti@0
|
24 }
|
|
kkonganti@0
|
25
|
|
kkonganti@0
|
26 if (params.mlst_run) {
|
|
kkonganti@0
|
27 withName: 'MLST' {
|
|
kkonganti@0
|
28 ext.args = addParamsToSummary(
|
|
kkonganti@0
|
29 loadThisFunction("${params.toolshelp}${params.fs}mlst.nf").mlstHelp(params).helpparams
|
|
kkonganti@0
|
30 )
|
|
kkonganti@0
|
31 }
|
|
kkonganti@0
|
32 }
|
|
kkonganti@0
|
33
|
|
kkonganti@0
|
34 if (params.mashsketch_run) {
|
|
kkonganti@0
|
35 withName: 'MASH_SKETCH' {
|
|
kkonganti@0
|
36 ext.args = addParamsToSummary(
|
|
kkonganti@0
|
37 loadThisFunction("${params.toolshelp}${params.fs}mashsketch.nf").mashsketchHelp(params).helpparams
|
|
kkonganti@0
|
38 )
|
|
kkonganti@0
|
39 }
|
|
kkonganti@0
|
40 }
|
|
kkonganti@0
|
41 }
|
|
kkonganti@0
|
42
|
|
kkonganti@0
|
43 // Method to instantiate a new function parser
|
|
kkonganti@0
|
44 // Need to refactor using ScriptParser... another day
|
|
kkonganti@0
|
45 def loadThisFunction (func_file) {
|
|
kkonganti@0
|
46 GroovyShell grvy_sh = new GroovyShell()
|
|
kkonganti@0
|
47 def func = grvy_sh.parse(new File ( func_file ) )
|
|
kkonganti@0
|
48 return func
|
|
kkonganti@0
|
49 }
|
|
kkonganti@0
|
50
|
|
kkonganti@0
|
51 // Method to add relevant final parameters to summary log
|
|
kkonganti@0
|
52 def addParamsToSummary(Map params_to_add = [:]) {
|
|
kkonganti@0
|
53
|
|
kkonganti@0
|
54 if (!params_to_add.isEmpty()) {
|
|
kkonganti@0
|
55 def not_null_params_to_add = params_to_add.findAll {
|
|
kkonganti@0
|
56 it.value.clivalue != null &&
|
|
kkonganti@0
|
57 it.value.clivalue != '[:]' &&
|
|
kkonganti@0
|
58 it.value.clivalue != ''
|
|
kkonganti@0
|
59 }
|
|
kkonganti@0
|
60
|
|
kkonganti@0
|
61 params.logtheseparams += not_null_params_to_add.keySet().toList()
|
|
kkonganti@0
|
62
|
|
kkonganti@0
|
63 return not_null_params_to_add.collect {
|
|
kkonganti@0
|
64 "${it.value.cliflag} ${it.value.clivalue.toString().replaceAll(/(?:^\s+|\s+$)/, '')}"
|
|
kkonganti@0
|
65 }.join(' ').trim()
|
|
kkonganti@0
|
66 }
|
|
kkonganti@0
|
67 return 1
|
|
kkonganti@0
|
68 } |
