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