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comparison 1.0.0/lib/help/salmonidx.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 salmon index within CPIPES.
2
3 def salmonidxHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'salmonidx_run': [
12 clihelp: 'Run `salmon index` tool. Default: ' +
13 (params.salmonidx_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'salmonidx_k': [
18 clihelp: 'The size of k-mers that should be used for the ' +
19 " quasi index. Default: ${params.salmonidx_k}",
20 cliflag: '-k',
21 clivalue: (params.salmonidx_k ?: '')
22 ],
23 'salmonidx_gencode': [
24 clihelp: 'This flag will expect the input transcript FASTA ' +
25 'to be in GENCODE format, and will split the transcript ' +
26 'name at the first `|` character. These reduced names ' +
27 'will be used in the output and when looking for these ' +
28 'transcripts in a gene to transcript GTF.' +
29 " Default: ${params.salmonidx_gencode}",
30 cliflag: '--gencode',
31 clivalue: (params.salmonidx_gencode ? ' ' : '')
32 ],
33 'salmonidx_features': [
34 clihelp: 'This flag will expect the input reference to be in the ' +
35 'tsv file format, and will split the feature name at the first ' +
36 '`tab` character. These reduced names will be used in the output ' +
37 'and when looking for the sequence of the features. GTF.' +
38 " Default: ${params.salmonidx_features}",
39 cliflag: '--features',
40 clivalue: (params.salmonidx_features ? ' ' : '')
41 ],
42 'salmonidx_keepDuplicates': [
43 clihelp: 'This flag will disable the default indexing behavior of ' +
44 'discarding sequence-identical duplicate transcripts. If this ' +
45 'flag is passed then duplicate transcripts that appear in the ' +
46 'input will be retained and quantified separately.' +
47 " Default: ${params.salmonidx_keepDuplicates}",
48 cliflag: '--keepDuplicates',
49 clivalue: (params.salmonidx_keepDuplicates ? ' ' : '')
50 ],
51 'salmonidx_keepFixedFasta': [
52 clihelp: 'Retain the fixed fasta file (without short ' +
53 'transcripts and duplicates, clipped, etc.) generated ' +
54 "during indexing. Default: ${params.salmonidx_keepFixedFasta}",
55 cliflag: '--keepFixedFasta',
56 clivalue: (params.salmonidx_keepFixedFasta ?: '')
57 ],
58 'salmonidx_filterSize': [
59 clihelp: 'The size of the Bloom filter that will be used ' +
60 'by TwoPaCo during indexing. The filter will be of ' +
61 'size 2^{filterSize}. A value of -1 means that the ' +
62 'filter size will be automatically set based on the ' +
63 'number of distinct k-mers in the input, as estimated by ' +
64 "nthll. Default: ${params.salmonidx_filterSize}",
65 cliflag: '--filterSize',
66 clivalue: (params.salmonidx_filterSize ?: '')
67 ],
68 'salmonidx_sparse': [
69 clihelp: 'Build the index using a sparse sampling of k-mer ' +
70 'positions This will require less memory (especially ' +
71 'during quantification), but will take longer to construct' +
72 'and can slow down mapping / alignment.' +
73 " Default: ${params.salmonidx_sparse}",
74 cliflag: '--sparse',
75 clivalue: (params.salmonidx_sparse ? ' ' : '')
76 ],
77 'salmonidx_n': [
78 clihelp: 'Do not clip poly-A tails from the ends of target ' +
79 "sequences. Default: ${params.salmonidx_n}",
80 cliflag: '-n',
81 clivalue: (params.salmonidx_n ? ' ' : '')
82 ]
83 ]
84
85 toolspecs.each {
86 k, v -> tool.text['--' + k] = "${v.clihelp}"
87 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
88 }
89
90 return tool
91 }