Mercurial > repos > galaxytrakr > hfp_bettercallsal_awsbatch

comparison 1.0.0/lib/help/bbmerge.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 bbmerge within CPIPES.
2
3 def bbmergeHelp(params) {
4
5 Map tool = [:]
6 Map toolspecs = [:]
7 tool.text = [:]
8 tool.helpparams = [:]
9
10 toolspecs = [
11 'bbmerge_run': [
12 clihelp: 'Run BBMerge tool. Default: ' +
13 (params.bbmerge_run ?: false),
14 cliflag: null,
15 clivalue: null
16 ],
17 'bbmerge_reads': [
18 clihelp: 'Quit after this many read pairs (-1 means all) ' +
19 "Default: ${params.bbmerge_reads}",
20 cliflag: 'reads=',
21 clivalue: (params.bbmerge_reads ?: '')
22 ],
23 'bbmerge_adapters': [
24 clihelp: 'Absolute UNIX path pointing to the adapters file in ' +
25 "FASTA format. Default: ${params.bbmerge_adapters}",
26 cliflag: 'adapters=',
27 clivalue: (params.bbmerge_adapters ?: '')
28 ],
29 'bbmerge_ziplevel': [
30 clihelp: 'Set to 1 (lowest) through 9 (max) to change compression ' +
31 "level; lower compression is faster. Default: ${params.bbmerge_ziplevel}",
32 cliflag: 'ziplevel=',
33 clivalue: (params.bbmerge_ziplevel ?: '')
34 ],
35 'bbmerge_ordered': [
36 clihelp: 'Output reads in the same order as input. ' +
37 "Default: ${params.bbmerge_ordered}",
38 cliflag: 'ordered=',
39 clivalue: (params.bbmerge_ordered ?: '')
40 ],
41 'bbmerge_qtrim': [
42 clihelp: 'Trim read ends to remove bases with quality below --bbmerge_minq. ' +
43 'Trims BEFORE merging. Values: t (trim both ends), ' +
44 'f (neither end), r (right end only), l (left end only). ' +
45 "Default: ${params.bbmerge_qtrim}",
46 cliflag: 'qtrim=',
47 clivalue: (params.bbmerge_qtrim ?: '')
48 ],
49 'bbmerge_qtrim2': [
50 clihelp: 'May be specified instead of --bbmerge_qtrim to perform trimming ' +
51 'only if merging is unsuccesful. then retry merging. ' +
52 "Default: ${params.bbmerge_qtrim2}",
53 cliflag: 'qtrim2=',
54 clivalue: (params.bbmerge_qtrim2 ?: '')
55 ],
56 'bbmerge_trimq': [
57 clihelp: 'Trim quality threshold. This may be comma-delimited list (ascending) ' +
58 "to try multiple values. Default: ${params.bbmerge_trimq}",
59 cliflag: 'trimq=',
60 clivalue: (params.bbmerge_trimq ?: '')
61 ],
62 'bbmerge_minlength': [
63 clihelp: '(ml) Reads shorter than this after trimming, but before ' +
64 'merging, will be discarded. Pairs will be discarded only' +
65 "if both are shorter. Default: ${params.bbmerge_minlength}",
66 cliflag: 'minlength=',
67 clivalue: (params.bbmerge_minlength ?: '')
68 ],
69 'bbmerge_tbo': [
70 clihelp: '(trimbyoverlap). Trim overlapping reads to remove right ' +
71 "most (3') non-overlaping portion instead of joining " +
72 "Default: ${params.bbmerge_tbo}",
73 cliflag: 'tbo=',
74 clivalue: (params.bbmerge_tbo ?: '')
75 ],
76 'bbmerge_minavgquality': [
77 clihelp: '(maq). Reads with average quality below this after trimming will ' +
78 "not be attempted to merge. Default: ${params.bbmerge_minavgquality}",
79 cliflag: 'minavgquality=',
80 clivalue: (params.bbmerge_minavgquality ?: '')
81 ],
82 'bbmerge_trimpolya': [
83 clihelp: 'Trim trailing poly-A tail from adapter output. Only affects ' +
84 'outadapter. This also trims poly-A followed by poly-G, which ' +
85 "occurs on NextSeq. Default: ${params.bbmerge_trimpolya}",
86 cliflag: 'trimpolya=',
87 clivalue: (params.bbmerge_trimpolya ?: '')
88 ],
89 'bbmerge_pfilter': [
90 clihelp: 'Ban improbable overlaps. Higher is more strict. 0 will ' +
91 'disable the filter; 1 will allow only perfect overlaps. ' +
92 "Default: ${params.bbmerge_pfilter}",
93 cliflag: 'pfilter=',
94 clivalue: (params.bbmerge_pfilter ?: '')
95 ],
96 'bbmerge_ouq': [
97 clihelp: 'Calculate best overlap using quality values. ' +
98 "Default: ${params.bbmerge_ouq}",
99 cliflag: 'ouq',
100 clivalue: (params.bbmerge_ouq ?: '')
101 ],
102 'bbmerge_owq': [
103 clihelp: 'Calculate best overlap without using quality values. ' +
104 "Default: ${params.bbmerge_owq}",
105 cliflag: 'owq=',
106 clivalue: (params.bbmerge_owq ?: '')
107 ],
108 'bbmerge_strict': [
109 clihelp: 'Decrease false positive rate and merging rate. ' +
110 "Default: ${params.bbmerge_strict}",
111 cliflag: 'strict=',
112 clivalue: (params.bbmerge_strict ?: '')
113 ],
114 'bbmerge_verystrict': [
115 clihelp: 'Greatly decrease false positive rate and merging rate. ' +
116 "Default: ${params.bbmerge_verystrict}",
117 cliflag: 'verystrict=',
118 clivalue: (params.bbmerge_verystrict ?: '')
119 ],
120 'bbmerge_ultrastrict': [
121 clihelp: 'Decrease false positive rate and merging rate even more. ' +
122 "Default: ${params.bbmerge_ultrastrict}",
123 cliflag: 'ultrastrict=',
124 clivalue: (params.bbmerge_ultrastrict ?: '')
125 ],
126 'bbmerge_maxstrict': [
127 clihelp: 'Maxiamally decrease false positive rate and merging rate. ' +
128 "Default: ${params.bbmerge_maxstrict}",
129 cliflag: 'maxstrict=',
130 clivalue: (params.bbmerge_maxstrict ?: '')
131 ],
132 'bbmerge_loose': [
133 clihelp: 'Increase false positive rate and merging rate. ' +
134 "Default: ${params.bbmerge_loose}",
135 cliflag: 'loose=',
136 clivalue: (params.bbmerge_loose ?: '')
137 ],
138 'bbmerge_veryloose': [
139 clihelp: 'Greatly increase false positive rate and merging rate. ' +
140 "Default: ${params.bbmerge_veryloose}",
141 cliflag: 'veryloose=',
142 clivalue: (params.bbmerge_veryloose ?: '')
143 ],
144 'bbmerge_ultraloose': [
145 clihelp: 'Increase false positive rate and merging rate even more. ' +
146 "Default: ${params.bbmerge_ultraloose}",
147 cliflag: 'ultraloose=',
148 clivalue: (params.bbmerge_ultraloose ?: '')
149 ],
150 'bbmerge_maxloose': [
151 clihelp: 'Maximally increase false positive rate and merging rate. ' +
152 "Default: ${params.bbmerge_maxloose}",
153 cliflag: 'maxloose=',
154 clivalue: (params.bbmerge_maxloose ?: '')
155 ],
156 'bbmerge_fast': [
157 clihelp: 'Fastest possible preset. ' +
158 "Default: ${params.bbmerge_fast}",
159 cliflag: 'fast=',
160 clivalue: (params.bbmerge_fast ?: '')
161 ],
162 'bbmerge_k': [
163 clihelp: 'Kmer length. 31 (or less) is fastest and uses the least ' +
164 'memory, but higher values may be more accurate. ' +
165 '60 tends to work well for 150bp reads. ' +
166 "Default: ${params.bbmerge_k}",
167 cliflag: 'k=',
168 clivalue: (params.bbmerge_k ?: '')
169 ],
170 'bbmerge_prealloc': [
171 clihelp: 'Pre-allocate memory rather than dynamically growing. ' +
172 'Faster and more memory-efficient for large datasets. ' +
173 'A float fraction (0-1) may be specified, default 1. ' +
174 "Default: ${params.bbmerge_prealloc}",
175 cliflag: 'prealloc=',
176 clivalue: (params.bbmerge_prealloc ?: '')
177 ]
178 ]
179
180 toolspecs.each {
181 k, v -> tool.text['--' + k] = "${v.clihelp}"
182 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
183 }
184
185 return tool
186 }