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comparison 1.0.0/lib/help/medakaconsensus.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 medaka `consensus` within CPIPES.
2
3 def medakaconsensusHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'medakaconsensus_run': [
12 clihelp: 'Run medaka `consensus` tool. Default: ' +
13 (params.medakaconsensus_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'medakaconsensus_batch_size': [
18 clihelp: 'Inference batch size. ' +
19 "Default: ${params.medakaconsensus_batch_size}",
20 cliflag: '--batch_size',
21 clivalue: (params.medakaconsensus_batch_size ?: '')
22 ],
23 'medakaconsensus_chunk_len': [
24 clihelp: 'Chunk length of samples. ' +
25 "Default: ${params.medakaconsensus_chunk_len}",
26 cliflag: '--chunk_len',
27 clivalue: (params.medakaconsensus_chunk_len ?: '')
28 ],
29 'medakaconsensus_chunk_ovlp': [
30 clihelp: 'Overlap of chunks. ' +
31 "Default: ${params.medakaconsensus_chunk_ovlp}",
32 cliflag: '--chunk_ovlp',
33 clivalue: (params.medakaconsensus_chunk_ovlp ?: '')
34 ],
35 'medakaconsensus_regions': [
36 clihelp: 'Genomic regions to analyze, or a bed file. ' +
37 "Default: ${params.medakaconsensus_regions}",
38 cliflag: '--regions',
39 clivalue: (params.medakaconsensus_regions ?: '')
40 ],
41 'medakaconsensus_model': [
42 clihelp: 'Model to use. Can be a medaka model name or a basecaller model name ' +
43 "suffixed with ':consensus' or ':variant'. " +
44 "Ex: 'dna_r10.4.1_e8.2_400bps_hac@v4.1.0:variant'. " +
45 "Default: ${params.medakaconsensus_model}",
46 cliflag: '--model',
47 clivalue: (params.medakaconsensus_model ?: '')
48 ],
49 'medakaconsensus_auto_model': [
50 clihelp: 'Automatically choose model according to input. Use one of ' +
51 "'consensus' or 'variant'. Default: ${params.medakaconsensus_auto_model}",
52 cliflag: '--auto_model',
53 clivalue: (params.medakaconsensus_auto_model ?: '')
54 ],
55 'medakaconsensus_bam_chunk': [
56 clihelp: 'Size of reference chunks each worker parses from bam. ' +
57 "Default: ${params.medakaconsensus_bam_chunk}",
58 cliflag: '--bam_chunk',
59 clivalue: (params.medakaconsensus_bam_chunk ?: '')
60 ],
61 'medakaconsensus_chk_out': [
62 clihelp: 'Verify integrity of output file after inference. ' +
63 "Default: ${params.medakaconsensus_chk_out}",
64 cliflag: '--check_output',
65 clivalue: (params.medakaconsensus_chk_out ? ' ' : '')
66 ],
67 'medakaconsensus_save_feats': [
68 clihelp: 'Save features with consensus probabilities. ' +
69 "Default: ${params.medakaconsensus_save_feats}",
70 cliflag: '--save_features',
71 clivalue: (params.medakaconsensus_save_feats ? ' ' : '')
72 ],
73 'medakaconsensus_read_grp': [
74 clihelp: "Read group to select. Default: ${params.medakaconsensus_read_grp}",
75 cliflag: '--RG',
76 clivalue: (params.medakaconsensus_read_grp ?: '')
77 ],
78 'medakaconsensus_tag_name': [
79 clihelp: "Two-letter tag name. Default: ${params.medakaconsensus_tag_name}",
80 cliflag: '--tag_name',
81 clivalue: (params.medakaconsensus_tag_name ?: '')
82 ],
83 'medakaconsensus_tag_val': [
84 clihelp: "Value of tag. Default: ${params.medakaconsensus_tag_val}",
85 cliflag: '--tag_val',
86 clivalue: (params.medakaconsensus_tag_val ?: '')
87 ],
88 'medakaconsensus_tag_keep': [
89 clihelp: 'Keep alignments when tag is missing. '
90 + "Default: ${params.medakaconsensus_tag_keep}",
91 cliflag: '--tag_keep_missing',
92 clivalue: (params.medakaconsensus_tag_keep ?: '')
93 ]
94 ]
95
96 toolspecs.each {
97 k, v -> tool.text['--' + k] = "${v.clihelp}"
98 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
99 }
100
101 return tool
102 }