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comparison 1.0.0/lib/help/spades.nf @ 0:0a8dda29956e draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 // Help text for spades within CPIPES.
2
3 def spadesHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'spades_run': [
12 clihelp: 'Run SPAdes assembler. Default: ' +
13 (params.spades_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'spades_isolate': [
18 clihelp: 'This flag is highly recommended for high-coverage isolate and ' +
19 "multi-cell data. Default: ${params.spades_isolate}",
20 cliflag: '--isolate',
21 clivalue: (params.spades_isolate ? ' ' : '')
22 ],
23 'spades_sc': [
24 clihelp: 'This flag is required for MDA (single-cell) data. ' +
25 "Default: ${params.spades_sc}",
26 cliflag: '--sc',
27 clivalue: (params.spades_sc ? ' ' : '')
28 ],
29 'spades_meta': [
30 clihelp: 'This flag is required for metagenomic data. ' +
31 "Default: ${params.spades_meta}",
32 cliflag: '--meta',
33 clivalue: (params.spades_meta ? ' ' : '')
34 ],
35 'spades_bio': [
36 clihelp: 'This flag is required for biosytheticSPAdes mode. ' +
37 "Default: ${params.spades_bio}",
38 cliflag: '--bio',
39 clivalue: (params.spades_bio ? ' ' : '')
40 ],
41 'spades_corona': [
42 clihelp: 'This flag is required for coronaSPAdes mode. ' +
43 "Default: ${params.spades_corona}",
44 cliflag: '--corona',
45 clivalue: (params.spades_corona ? ' ' : '')
46 ],
47 'spades_rna': [
48 clihelp: 'This flag is required for RNA-Seq data. ' +
49 "Default: ${params.spades_rna}",
50 cliflag: '--rna',
51 clivalue: (params.spades_rna ? ' ' : '')
52 ],
53 'spades_plasmid': [
54 clihelp: 'Runs plasmidSPAdes pipeline for plasmid detection. ' +
55 "Default: ${params.spades_plasmid}",
56 cliflag: '--plasmid',
57 clivalue: (params.spades_plasmid ? ' ' : '')
58 ],
59 'spades_metaviral': [
60 clihelp: 'Runs metaviralSPAdes pipeline for virus detection. ' +
61 "Default: ${params.spades_metaviral}",
62 cliflag: '--metaviral',
63 clivalue: (params.spades_metaviral ? ' ' : '')
64 ],
65 'spades_metaplasmid': [
66 clihelp: 'Runs metaplasmidSPAdes pipeline for plasmid detection in ' +
67 "metagenomics datasets. Default: ${params.spades_metaplasmid}",
68 cliflag: '--metaplasmid',
69 clivalue: (params.spades_metaplasmid ? ' ' : '')
70 ],
71 'spades_rnaviral': [
72 clihelp: 'This flag enables virus assembly module from RNA-Seq data. ' +
73 "Default: ${params.spades_rnaviral}",
74 cliflag: '--rnaviral',
75 clivalue: (params.spades_rnaviral ? ' ' : '')
76 ],
77 'spades_iontorrent': [
78 clihelp: 'This flag is required for IonTorrent data. ' +
79 "Default: ${params.spades_iontorrent}",
80 cliflag: '--iontorrent',
81 clivalue: (params.spades_iontorrent ? ' ' : '')
82 ],
83 'spades_only_assembler': [
84 clihelp: 'Runs only the SPAdes assembler module (without read error correction). ' +
85 "Default: ${params.spades_only_assembler}",
86 cliflag: '--only-assembler',
87 clivalue: (params.spades_only_assembler ? ' ' : '')
88 ],
89 'spades_careful': [
90 clihelp: 'Tries to reduce the number of mismatches and short indels in the assembly. ' +
91 "Default: ${params.spades_careful}",
92 cliflag: '--careful',
93 clivalue: (params.spades_careful ? ' ' : '')
94 ],
95 'spades_cov_cutoff': [
96 clihelp: 'Coverage cutoff value (a positive float number). ' +
97 "Default: ${params.spades_cov_cutoff}",
98 cliflag: '--cov-cutoff',
99 clivalue: (params.spades_cov_cutoff ?: '')
100 ],
101 'spades_k': [
102 clihelp: 'List of k-mer sizes (must be odd and less than 128). ' +
103 "Default: ${params.spades_k}",
104 cliflag: '-k',
105 clivalue: (params.spades_k ?: '')
106 ],
107 'spades_hmm': [
108 clihelp: 'Directory with custom hmms that replace the default ones (very rare). ' +
109 "Default: ${params.spades_hmm}",
110 cliflag: '--custom-hmms',
111 clivalue: (params.spades_hmm ?: '')
112 ]
113 ]
114
115 toolspecs.each {
116 k, v -> tool.text['--' + k] = "${v.clihelp}"
117 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
118 }
119
120 return tool
121 }