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comparison 1.0.0/lib/help/filtlong.nf @ 0:801b85b03a17 draft default tip

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author galaxytrakr
date Thu, 28 May 2026 20:31:42 +0000
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-1:000000000000 0:801b85b03a17
1 // Help text for filtlong within CPIPES.
2
3 def filtlongHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'filtlong_run': [
12 clihelp: 'Run filtlong read trimming tool. Default: ' +
13 (params.filtlong_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'filtlong_keep_perc': [
18 clihelp: 'Keep only this percentage of best reads. ' +
19 "Default: ${params.filtlong_keep_perc}",
20 cliflag: '--keep_percent',
21 clivalue: (params.filtlong_keep_perc ?: '')
22 ],
23 'filtlong_target_bases': [
24 clihelp: 'Keep only the best bases up to this many total bases. ' +
25 "Default: ${params.filtlong_target_bases}",
26 cliflag: '--target_bases',
27 clivalue: (params.filtlong_target_bases ?: '')
28 ],
29 'filtlong_min_length': [
30 clihelp: 'Minimum length threshold. ' +
31 "Default: ${params.filtlong_min_length}",
32 cliflag: '--min_length',
33 clivalue: (params.filtlong_min_length ?: '')
34 ],
35 'filtlong_max_length': [
36 clihelp: 'Maximum length threshold. ' +
37 "Default: ${params.filtlong_max_length}",
38 cliflag: '--max_length',
39 clivalue: (params.filtlong_max_length ?: '')
40 ],
41 'filtlong_min_mean_q': [
42 clihelp: 'Minimum mean quality threshold. ' +
43 "Default: ${params.filtlong_min_mean_q}",
44 cliflag: '--min_mean_q',
45 clivalue: (params.filtlong_min_mean_q ?: '')
46 ],
47 'filtlong_min_window_q': [
48 clihelp: 'Minimum window quality threshold. ' +
49 "Default: ${params.filtlong_min_window_q}",
50 cliflag: '--min_window_q',
51 clivalue: (params.filtlong_min_window_q ?: '')
52 ],
53 'filtlong_a': [
54 clihelp: "External reference assembly in FASTA format. " +
55 "Default: ${params.filtlong_a}",
56 cliflag: '-a',
57 clivalue: (params.filtlong_a ?: '')
58 ],
59 'filtlong_1': [
60 clihelp: 'External reference Illumina reads in FASTQ format (R1). ' +
61 "Default: ${params.filtlong_1}",
62 cliflag: '-1',
63 clivalue: (params.filtlong_1 ?: '')
64 ],
65 'filtlong_2': [
66 clihelp: 'External reference Illumina reads in FASTQ format (R2). ' +
67 "Default: ${params.filtlong_2}",
68 cliflag: '--2',
69 clivalue: (params.filtlong_2 ?: '')
70 ],
71 'filtlong_len_weight': [
72 clihelp: 'Weight given to the length score. ' +
73 "Default: ${params.filtlong_len_weight}",
74 cliflag: '--length_weight',
75 clivalue: (params.filtlong_len_weight ?: '')
76 ],
77 'filtlong_mean_q_weight': [
78 clihelp: 'Weight given to the mean quality score. ' +
79 "Default: ${params.filtlong_mean_q_weight}",
80 cliflag: '--mean_q_weight',
81 clivalue: (params.filtlong_mean_q_weight ?: '')
82 ],
83 'filtlong_window_q_weight': [
84 clihelp: 'Weight given to the window quality score. ' +
85 "Default: ${params.filtlong_window_q_weight}",
86 cliflag: '--window_q_weight',
87 clivalue: (params.filtlong_window_q_weight ?: '')
88 ],
89 'filtlong_trim': [
90 clihelp: 'Trim non k-mer matching bases from start/end of the reads. ' +
91 "Default: ${params.filtlong_trim}",
92 cliflag: '--trim',
93 clivalue: (params.filtlong_trim ? ' ' : '')
94 ],
95 'filtlong_split': [
96 clihelp: 'Split reads at this many (or more) consecutive non k-mer matching bases. ' +
97 "Default: ${params.filtlong_split}",
98 cliflag: '--split',
99 clivalue: (params.filtlong_split ? ' ' : '')
100 ],
101 'filtlong_window_size': [
102 clihelp: 'Size of sliding window used when measuring window quality. ' +
103 "Default: ${params.filtlong_window_size}",
104 cliflag: '--window_size',
105 clivalue: (params.filtlong_window_size ?: '')
106 ]
107 ]
108
109 toolspecs.each {
110 k, v -> tool.text['--' + k] = "${v.clihelp}"
111 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
112 }
113
114 return tool
115 }