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comparison 0.2.0/lib/help/masurcapolca.nf @ 0:9e8b1c747a6a draft default tip

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author galaxytrakr
date Fri, 29 May 2026 13:32:17 +0000
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-1:000000000000 0:9e8b1c747a6a
1 // Help text for `masurca's polca.sh` within CPIPES.
2
3 def masurcapolcaHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'masurcapolca_run': [
12 clihelp: 'Run `polca.sh` from masurca. Default: ' +
13 (params.masurcapolca_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'masurcapolca_n': [
18 clihelp: 'Do not polish, just create vcf file, evaluate the assembly and exit. ' +
19 "Default: ${params.masurcapolca_n}",
20 cliflag: '-n',
21 clivalue: (params.masurcapolca_n ? ' ' : '')
22 ]
23 ]
24
25 toolspecs.each {
26 k, v -> tool.text['--' + k] = "${v.clihelp}"
27 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
28 }
29
30 return tool
31 }