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comparison 1.0.0/lib/help/seqsero2.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 def seqsero2Help(params) {
2
3 Map tool = [:]
4 Map toolspecs = [:]
5 tool.text = [:]
6 tool.helpparams = [:]
7
8 toolspecs = [
9 'seqsero2_run': [
10 clihelp: "Run SeqSero2 tool. Default: ${params.seqsero2_run}",
11 cliflag: null,
12 clivalue: null
13 ],
14 'seqsero2_t': [
15 clihelp: "'1' for interleaved paired-end reads, '2' for " +
16 "separated paired-end reads, '3' for single reads, '4' for " +
17 "genome assembly, '5' for nanopore reads (fasta/fastq). " +
18 "Default: ${params.seqsero2_t}",
19 cliflag: '-t',
20 clivalue: (params.seqsero2_t ?: '')
21 ],
22 'seqsero2_m': [
23 clihelp: "Which workflow to apply, 'a'(raw reads allele " +
24 "micro-assembly), 'k'(raw reads and genome assembly k-mer). " +
25 "Default: ${params.seqsero2_m}",
26 cliflag: '-m',
27 clivalue: (params.seqsero2_m ?: '')
28 ],
29 'seqsero2_c': [
30 clihelp: 'SeqSero2 will only output serotype prediction without the directory ' +
31 'containing log files. ' +
32 "Default: ${params.seqsero2_c}",
33 cliflag: '-c',
34 clivalue: (params.seqsero2_c ? ' ' : '')
35 ],
36 'seqsero2_s': [
37 clihelp: 'SeqSero2 will not output header in SeqSero_result.tsv. ' +
38 "Default: ${params.seqsero2_s}",
39 cliflag: '-l',
40 clivalue: (params.seqsero2_s ? ' ' : '')
41 ]
42 ]
43
44 toolspecs.each {
45 k, v -> tool.text['--' + k] = "${v.clihelp}"
46 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
47 }
48
49 return tool
50 }