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comparison 1.0.0/lib/help/centrifuge.nf @ 0:801b85b03a17 draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 // Help text for centrifuge within CPIPES.
2
3 def centrifugeHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'centrifuge_x': [
12 clihelp: "Absolute path to centrifuge database. Default: ${params.centrifuge_x}",
13 cliflag: '-x',
14 clivalue: null
15 ],
16 'centrifuge_save_unaligned': [
17 clihelp: 'Save SINGLE-END reads that did not align. For PAIRED-END' +
18 " reads, save read pairs that did not align concordantly. Default: ${params.centrifuge_save_unaligned}",
19 cliflag: null, // Handled in modules logic.
20 clivalue: null
21 ],
22 'centrifuge_save_aligned': [
23 clihelp: 'Save SINGLE-END reads that aligned. For PAIRED-END' +
24 " reads, save read pairs that aligned concordantly. Default: ${params.centrifuge_save_aligned}",
25 cliflag: null, // Handled in modules logic.
26 clivalue: null
27 ],
28 'centrifuge_out_fmt_sam': [
29 clihelp: "Centrifuge output should be in SAM. Default: ${params.centrifuge_save_aligned}",
30 cliflag: null, // Handled in modules logic.
31 clivalue: null
32 ],
33 'centrifuge_extract_bug': [
34 clihelp: "Extract this bug from centrifuge results." +
35 " Default: ${params.centrifuge_extract_bug}",
36 cliflag: null, // Handled in modules logic.
37 clivalue: null,
38 ],
39 'centrifuge_ignore_quals': [
40 clihelp: 'Treat all quality values as 30 on Phred scale. ' +
41 "Default: ${params.centrifuge_ignore_quals}",
42 cliflag: '--ignore-quals',
43 clivalue: (params.centrifuge_ignore_quals ? ' ' : '')
44 ]
45 ]
46
47 toolspecs.each {
48 k, v -> tool.text['--' + k] = "${v.clihelp}"
49 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
50 }
51
52 return tool
53 }
54