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annotate 0.7.0/lib/help/bbmerge.nf @ 17:0e7a0053e4a6

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author kkonganti
date Mon, 15 Jul 2024 10:42:02 -0400
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kkonganti@17 1 // Help text for bbmerge within CPIPES.
kkonganti@17 2
kkonganti@17 3 def bbmergeHelp(params) {
kkonganti@17 4
kkonganti@17 5 Map tool = [:]
kkonganti@17 6 Map toolspecs = [:]
kkonganti@17 7 tool.text = [:]
kkonganti@17 8 tool.helpparams = [:]
kkonganti@17 9
kkonganti@17 10 toolspecs = [
kkonganti@17 11 'bbmerge_run': [
kkonganti@17 12 clihelp: 'Run BBMerge tool. Default: ' +
kkonganti@17 13 (params.bbmerge_run ?: false),
kkonganti@17 14 cliflag: null,
kkonganti@17 15 clivalue: null
kkonganti@17 16 ],
kkonganti@17 17 'bbmerge_reads': [
kkonganti@17 18 clihelp: 'Quit after this many read pairs (-1 means all) ' +
kkonganti@17 19 "Default: ${params.bbmerge_reads}",
kkonganti@17 20 cliflag: 'reads=',
kkonganti@17 21 clivalue: (params.bbmerge_reads ?: '')
kkonganti@17 22 ],
kkonganti@17 23 'bbmerge_adapters': [
kkonganti@17 24 clihelp: 'Absolute UNIX path pointing to the adapters file in ' +
kkonganti@17 25 "FASTA format. Default: ${params.bbmerge_adapters}",
kkonganti@17 26 cliflag: 'adapters=',
kkonganti@17 27 clivalue: (params.bbmerge_adapters ?: '')
kkonganti@17 28 ],
kkonganti@17 29 'bbmerge_ziplevel': [
kkonganti@17 30 clihelp: 'Set to 1 (lowest) through 9 (max) to change compression ' +
kkonganti@17 31 "level; lower compression is faster. Default: ${params.bbmerge_ziplevel}",
kkonganti@17 32 cliflag: 'ziplevel=',
kkonganti@17 33 clivalue: (params.bbmerge_ziplevel ?: '')
kkonganti@17 34 ],
kkonganti@17 35 'bbmerge_ordered': [
kkonganti@17 36 clihelp: 'Output reads in the same order as input. ' +
kkonganti@17 37 "Default: ${params.bbmerge_ordered}",
kkonganti@17 38 cliflag: 'ordered=',
kkonganti@17 39 clivalue: (params.bbmerge_ordered ?: '')
kkonganti@17 40 ],
kkonganti@17 41 'bbmerge_qtrim': [
kkonganti@17 42 clihelp: 'Trim read ends to remove bases with quality below --bbmerge_minq. ' +
kkonganti@17 43 'Trims BEFORE merging. Values: t (trim both ends), ' +
kkonganti@17 44 'f (neither end), r (right end only), l (left end only). ' +
kkonganti@17 45 "Default: ${params.bbmerge_qtrim}",
kkonganti@17 46 cliflag: 'qtrim=',
kkonganti@17 47 clivalue: (params.bbmerge_qtrim ?: '')
kkonganti@17 48 ],
kkonganti@17 49 'bbmerge_qtrim2': [
kkonganti@17 50 clihelp: 'May be specified instead of --bbmerge_qtrim to perform trimming ' +
kkonganti@17 51 'only if merging is unsuccesful. then retry merging. ' +
kkonganti@17 52 "Default: ${params.bbmerge_qtrim2}",
kkonganti@17 53 cliflag: 'qtrim2=',
kkonganti@17 54 clivalue: (params.bbmerge_qtrim2 ?: '')
kkonganti@17 55 ],
kkonganti@17 56 'bbmerge_trimq': [
kkonganti@17 57 clihelp: 'Trim quality threshold. This may be comma-delimited list (ascending) ' +
kkonganti@17 58 "to try multiple values. Default: ${params.bbmerge_trimq}",
kkonganti@17 59 cliflag: 'trimq=',
kkonganti@17 60 clivalue: (params.bbmerge_trimq ?: '')
kkonganti@17 61 ],
kkonganti@17 62 'bbmerge_minlength': [
kkonganti@17 63 clihelp: '(ml) Reads shorter than this after trimming, but before ' +
kkonganti@17 64 'merging, will be discarded. Pairs will be discarded only' +
kkonganti@17 65 "if both are shorter. Default: ${params.bbmerge_minlength}",
kkonganti@17 66 cliflag: 'minlength=',
kkonganti@17 67 clivalue: (params.bbmerge_minlength ?: '')
kkonganti@17 68 ],
kkonganti@17 69 'bbmerge_tbo': [
kkonganti@17 70 clihelp: '(trimbyoverlap). Trim overlapping reads to remove right ' +
kkonganti@17 71 "most (3') non-overlaping portion instead of joining " +
kkonganti@17 72 "Default: ${params.bbmerge_tbo}",
kkonganti@17 73 cliflag: 'tbo=',
kkonganti@17 74 clivalue: (params.bbmerge_tbo ?: '')
kkonganti@17 75 ],
kkonganti@17 76 'bbmerge_minavgquality': [
kkonganti@17 77 clihelp: '(maq). Reads with average quality below this after trimming will ' +
kkonganti@17 78 "not be attempted to merge. Default: ${params.bbmerge_minavgquality}",
kkonganti@17 79 cliflag: 'minavgquality=',
kkonganti@17 80 clivalue: (params.bbmerge_minavgquality ?: '')
kkonganti@17 81 ],
kkonganti@17 82 'bbmerge_trimpolya': [
kkonganti@17 83 clihelp: 'Trim trailing poly-A tail from adapter output. Only affects ' +
kkonganti@17 84 'outadapter. This also trims poly-A followed by poly-G, which ' +
kkonganti@17 85 "occurs on NextSeq. Default: ${params.bbmerge_trimpolya}",
kkonganti@17 86 cliflag: 'trimpolya=',
kkonganti@17 87 clivalue: (params.bbmerge_trimpolya ?: '')
kkonganti@17 88 ],
kkonganti@17 89 'bbmerge_pfilter': [
kkonganti@17 90 clihelp: 'Ban improbable overlaps. Higher is more strict. 0 will ' +
kkonganti@17 91 'disable the filter; 1 will allow only perfect overlaps. ' +
kkonganti@17 92 "Default: ${params.bbmerge_pfilter}",
kkonganti@17 93 cliflag: 'pfilter=',
kkonganti@17 94 clivalue: (params.bbmerge_pfilter ?: '')
kkonganti@17 95 ],
kkonganti@17 96 'bbmerge_ouq': [
kkonganti@17 97 clihelp: 'Calculate best overlap using quality values. ' +
kkonganti@17 98 "Default: ${params.bbmerge_ouq}",
kkonganti@17 99 cliflag: 'ouq',
kkonganti@17 100 clivalue: (params.bbmerge_ouq ?: '')
kkonganti@17 101 ],
kkonganti@17 102 'bbmerge_owq': [
kkonganti@17 103 clihelp: 'Calculate best overlap without using quality values. ' +
kkonganti@17 104 "Default: ${params.bbmerge_owq}",
kkonganti@17 105 cliflag: 'owq=',
kkonganti@17 106 clivalue: (params.bbmerge_owq ?: '')
kkonganti@17 107 ],
kkonganti@17 108 'bbmerge_strict': [
kkonganti@17 109 clihelp: 'Decrease false positive rate and merging rate. ' +
kkonganti@17 110 "Default: ${params.bbmerge_strict}",
kkonganti@17 111 cliflag: 'strict=',
kkonganti@17 112 clivalue: (params.bbmerge_strict ?: '')
kkonganti@17 113 ],
kkonganti@17 114 'bbmerge_verystrict': [
kkonganti@17 115 clihelp: 'Greatly decrease false positive rate and merging rate. ' +
kkonganti@17 116 "Default: ${params.bbmerge_verystrict}",
kkonganti@17 117 cliflag: 'verystrict=',
kkonganti@17 118 clivalue: (params.bbmerge_verystrict ?: '')
kkonganti@17 119 ],
kkonganti@17 120 'bbmerge_ultrastrict': [
kkonganti@17 121 clihelp: 'Decrease false positive rate and merging rate even more. ' +
kkonganti@17 122 "Default: ${params.bbmerge_ultrastrict}",
kkonganti@17 123 cliflag: 'ultrastrict=',
kkonganti@17 124 clivalue: (params.bbmerge_ultrastrict ?: '')
kkonganti@17 125 ],
kkonganti@17 126 'bbmerge_maxstrict': [
kkonganti@17 127 clihelp: 'Maxiamally decrease false positive rate and merging rate. ' +
kkonganti@17 128 "Default: ${params.bbmerge_maxstrict}",
kkonganti@17 129 cliflag: 'maxstrict=',
kkonganti@17 130 clivalue: (params.bbmerge_maxstrict ?: '')
kkonganti@17 131 ],
kkonganti@17 132 'bbmerge_loose': [
kkonganti@17 133 clihelp: 'Increase false positive rate and merging rate. ' +
kkonganti@17 134 "Default: ${params.bbmerge_loose}",
kkonganti@17 135 cliflag: 'loose=',
kkonganti@17 136 clivalue: (params.bbmerge_loose ?: '')
kkonganti@17 137 ],
kkonganti@17 138 'bbmerge_veryloose': [
kkonganti@17 139 clihelp: 'Greatly increase false positive rate and merging rate. ' +
kkonganti@17 140 "Default: ${params.bbmerge_veryloose}",
kkonganti@17 141 cliflag: 'veryloose=',
kkonganti@17 142 clivalue: (params.bbmerge_veryloose ?: '')
kkonganti@17 143 ],
kkonganti@17 144 'bbmerge_ultraloose': [
kkonganti@17 145 clihelp: 'Increase false positive rate and merging rate even more. ' +
kkonganti@17 146 "Default: ${params.bbmerge_ultraloose}",
kkonganti@17 147 cliflag: 'ultraloose=',
kkonganti@17 148 clivalue: (params.bbmerge_ultraloose ?: '')
kkonganti@17 149 ],
kkonganti@17 150 'bbmerge_maxloose': [
kkonganti@17 151 clihelp: 'Maximally increase false positive rate and merging rate. ' +
kkonganti@17 152 "Default: ${params.bbmerge_maxloose}",
kkonganti@17 153 cliflag: 'maxloose=',
kkonganti@17 154 clivalue: (params.bbmerge_maxloose ?: '')
kkonganti@17 155 ],
kkonganti@17 156 'bbmerge_fast': [
kkonganti@17 157 clihelp: 'Fastest possible preset. ' +
kkonganti@17 158 "Default: ${params.bbmerge_fast}",
kkonganti@17 159 cliflag: 'fast=',
kkonganti@17 160 clivalue: (params.bbmerge_fast ?: '')
kkonganti@17 161 ],
kkonganti@17 162 'bbmerge_k': [
kkonganti@17 163 clihelp: 'Kmer length. 31 (or less) is fastest and uses the least ' +
kkonganti@17 164 'memory, but higher values may be more accurate. ' +
kkonganti@17 165 '60 tends to work well for 150bp reads. ' +
kkonganti@17 166 "Default: ${params.bbmerge_k}",
kkonganti@17 167 cliflag: 'k=',
kkonganti@17 168 clivalue: (params.bbmerge_k ?: '')
kkonganti@17 169 ],
kkonganti@17 170 'bbmerge_prealloc': [
kkonganti@17 171 clihelp: 'Pre-allocate memory rather than dynamically growing. ' +
kkonganti@17 172 'Faster and more memory-efficient for large datasets. ' +
kkonganti@17 173 'A float fraction (0-1) may be specified, default 1. ' +
kkonganti@17 174 "Default: ${params.bbmerge_prealloc}",
kkonganti@17 175 cliflag: 'prealloc=',
kkonganti@17 176 clivalue: (params.bbmerge_prealloc ?: '')
kkonganti@17 177 ]
kkonganti@17 178 ]
kkonganti@17 179
kkonganti@17 180 toolspecs.each {
kkonganti@17 181 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17 182 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17 183 }
kkonganti@17 184
kkonganti@17 185 return tool
kkonganti@17 186 }