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comparison 0.2.0/lib/help/shovill.nf @ 11:a5f31c44f8c9

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author kkonganti
date Mon, 15 Jul 2024 16:11:44 -0400
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10:ddf7a172bf30 11:a5f31c44f8c9
1 // Help text for shovill within CPIPES.
2
3 def shovillHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'shovill_run': [
12 clihelp: 'Run shovill tool. Default: ' +
13 (params.shovill_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'shovill_depth': [
18 clihelp: 'Sub-sample R1/R2 to this depth. Disable with --shovill_depth 0. ' +
19 "Default: ${params.shovill_depth}",
20 cliflag: '--depth',
21 clivalue: (params.shovill_depth ?: 150)
22 ],
23 'shovill_gsize': [
24 clihelp: 'Estimated genome size eg. 3.2M. <false=AUTODETECT>. ' +
25 "Default: ${params.shovill_gsize}",
26 cliflag: '--gsize',
27 clivalue: (params.shovill_gsize ?: '')
28 ],
29 'shovill_minlen': [
30 clihelp: 'Minimum contig length. <false=AUTO>. ' +
31 "Default: ${params.shovill_minlen}",
32 cliflag: '--minlen',
33 clivalue: (params.shovill_minlen ?: '')
34 ],
35 'shovill_mincov': [
36 clihelp: "Minimum contig coverage. <false=AUTO>. " +
37 "Default: ${params.shovill_mincov}",
38 cliflag: '--mincov',
39 clivalue: (params.shovill_mincov ?: '')
40 ],
41 'shovill_namefmt': [
42 clihelp: "Format of contig FASTA IDs in 'printf' style. " +
43 "Default: ${params.shovill_namefmt}",
44 cliflag: '--namefmt',
45 clivalue: (params.shovill_namefmt ?: '')
46 ],
47 'shovill_keepfiles': [
48 clihelp: 'Keep intermediate files. ' +
49 "Default: ${params.shovill_keepfiles}",
50 cliflag: '--keepfiles',
51 clivalue: (params.shovill_keepfiles ? ' ' : '')
52 ],
53 'shovill_assembler': [
54 clihelp: 'Assembler: skesa, megahit, velvet, or spades. ' +
55 "Default: ${params.shovill_assembler}",
56 cliflag: '--assembler',
57 clivalue: (params.shovill_assembler ?: '')
58 ],
59 'shovill_opts': [
60 clihelp: "Extra assembler options in quotes. Ex: '--sc'. " +
61 "Default: ${params.shovill_opts}",
62 cliflag: '--opts',
63 clivalue: (params.shovill_opts ?: '')
64 ],
65 'shovill_kmers': [
66 clihelp: 'K-mers to use. <false=AUTO>. ' +
67 "Default: ${params.shovill_kmers}",
68 cliflag: '--kmers',
69 clivalue: (params.shovill_kmers ?: '')
70 ],
71 'shovill_trim': [
72 clihelp: 'Enable adator trimming. ' +
73 "Default: ${params.shovill_trim}",
74 cliflag: '--trim',
75 clivalue: (params.shovill_trim ? ' ' : '')
76 ],
77 'shovill_noreadcorr': [
78 clihelp: 'Disable read error correction. ' +
79 "Default: ${params.shovill_noreadcorr}",
80 cliflag: '--noreadcorr',
81 clivalue: (params.shovill_noreadcorr ? ' ' : '')
82 ],
83 'shovill_nostitch': [
84 clihelp: 'Disable read stitching. ' +
85 "Default: ${params.shovill_nostitch}",
86 cliflag: '--nostitch',
87 clivalue: (params.shovill_nostitch ? ' ' : '')
88 ],
89 'shovill_nocorr': [
90 clihelp: 'Disable post-assembly correction. ' +
91 "Default: ${params.shovill_nocorr}",
92 cliflag: '--nocorr',
93 clivalue: (params.shovill_nocorr ? ' ' : '')
94 ]
95 ]
96
97 toolspecs.each {
98 k, v -> tool.text['--' + k] = "${v.clihelp}"
99 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
100 }
101
102 return tool
103 }