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comparison 1.0.0/lib/help/seqkitrmdup.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 seqkit rmdup within CPIPES.
2
3 def seqkitrmdupHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'seqkit_rmdup_run': [
12 clihelp: 'Remove duplicate sequences using seqkit rmdup. Default: ' +
13 (params.seqkit_rmdup_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'seqkit_rmdup_n': [
18 clihelp: 'Match and remove duplicate sequences by full name instead of just ID. ' +
19 "Default: ${params.seqkit_rmdup_n}",
20 cliflag: '-n',
21 clivalue: (params.seqkit_rmdup_n ? ' ' : '')
22 ],
23 'seqkit_rmdup_s': [
24 clihelp: 'Match and remove duplicate sequences by sequence content. ' +
25 "Default: ${params.seqkit_rmdup_s}",
26 cliflag: '-s',
27 clivalue: (params.seqkit_rmdup_s ? ' ' : '')
28 ],
29 'seqkit_rmdup_d': [
30 clihelp: 'Save the duplicated sequences to a file. ' +
31 "Default: ${params.seqkit_rmdup_d}",
32 cliflag: null,
33 clivalue: null
34 ],
35 'seqkit_rmdup_D': [
36 clihelp: 'Save the number and list of duplicated sequences to a file. ' +
37 "Default: ${params.seqkit_rmdup_D}",
38 cliflag: null,
39 clivalue: null
40 ],
41 'seqkit_rmdup_i': [
42 clihelp: 'Ignore case while using seqkit rmdup. ' +
43 "Default: ${params.seqkit_rmdup_i}",
44 cliflag: '-i',
45 clivalue: (params.seqkit_rmdup_i ? ' ' : '')
46 ],
47 'seqkit_rmdup_P': [
48 clihelp: "Only consider positive strand (i.e. 5') when comparing by sequence content. " +
49 "Default: ${params.seqkit_rmdup_P}",
50 cliflag: '-P',
51 clivalue: (params.seqkit_rmdup_P ? ' ' : '')
52 ]
53 ]
54
55 toolspecs.each {
56 k, v -> tool.text['--' + k] = "${v.clihelp}"
57 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
58 }
59
60 return tool
61 }