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comparison 0.7.0/lib/help/flye.nf @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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16:b90e5a7a3d4f 17:0e7a0053e4a6
1 // Help text for flye within CPIPES.
2
3 def flyeHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'flye_pacbio_raw': [
12 clihelp: 'Input FASTQ reads are PacBio regular CLR reads (<20% error) ' +
13 "Default: ${params.flye_pacbio_raw}",
14 cliflag: '--pacbio-raw',
15 clivalue: (params.flye_pacbio_raw ? ' ' : '')
16 ],
17 'flye_pacbio_corr': [
18 clihelp: 'Input FASTQ reads are PacBio reads that were corrected ' +
19 "with other methods (<3% error). Default: ${params.flye_pacbio_corr}",
20 cliflag: '--pacbio-corr',
21 clivalue: (params.flye_pacbio_corr ? ' ' : '')
22 ],
23 'flye_pacbio_hifi': [
24 clihelp: 'Input FASTQ reads are PacBio HiFi reads (<1% error). ' +
25 "Default: ${params.flye_pacbio_hifi}",
26 cliflag: '--pacbio-hifi',
27 clivalue: (params.flye_pacbio_hifi ? ' ' : '')
28 ],
29 'flye_nano_raw': [
30 clihelp: 'Input FASTQ reads are ONT regular reads, pre-Guppy5 (<20% error). ' +
31 "Default: ${params.flye_nano_raw}",
32 cliflag: '--nano-raw',
33 clivalue: (params.flye_nano_raw ? ' ' : '')
34 ],
35 'flye_nano_corr': [
36 clihelp: 'Input FASTQ reads are ONT reads that were corrected with other ' +
37 "methods (<3% error). Default: ${params.flye_nano_corr}",
38 cliflag: '--nano-corr',
39 clivalue: (params.flye_nano_corr ? ' ' : '')
40 ],
41 'flye_nano_hq': [
42 clihelp: 'Input FASTQ reads are ONT high-quality reads: ' +
43 "Guppy5+ SUP or Q20 (<5% error). Default: ${params.flye_nano_hq}",
44 cliflag: '--nano-hq',
45 clivalue: (params.flye_nano_hq ? ' ' : '')
46 ],
47 'flye_genome_size': [
48 clihelp: 'Estimated genome size (for example, 5m or 2.6g). ' +
49 "Default: ${params.flye_genome_size}",
50 cliflag: '--genome-size',
51 clivalue: (params.flye_genome_size ?: '')
52 ],
53 'flye_polish_iter': [
54 clihelp: 'Number of genome polishing iterations. ' +
55 "Default: ${params.flye_polish_iter}",
56 cliflag: '--iterations',
57 clivalue: (params.flye_polish_iter ?: '')
58 ],
59 'flye_meta': [
60 clihelp: "Do a metagenome assembly (unenven coverage mode). Default: ${params.flye_meta}",
61 cliflag: '--meta',
62 clivalue: (params.flye_meta ? ' ' : '')
63 ],
64 'flye_min_overlap': [
65 clihelp: "Minimum overlap between reads. Default: ${params.flye_min_overlap}",
66 cliflag: '--min-overlap',
67 clivalue: (params.flye_min_overlap ?: '')
68 ],
69 'flye_scaffold': [
70 clihelp: "Enable scaffolding using assembly graph. Default: ${params.flye_scaffold}",
71 cliflag: '--scaffold',
72 clivalue: (params.flye_scaffold ? ' ' : '')
73 ]
74 ]
75
76 toolspecs.each {
77 k, v -> tool.text['--' + k] = "${v.clihelp}"
78 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
79 }
80
81 return tool
82 }