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annotate 0.4.2/lib/help/flye.nf @ 143:620bffa66bbb tip

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author kkonganti
date Thu, 11 Jul 2024 14:48:07 -0400
parents 52045ea4679d
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kkonganti@105 1 // Help text for flye within CPIPES.
kkonganti@105 2
kkonganti@105 3 def flyeHelp(params) {
kkonganti@105 4
kkonganti@105 5 Map tool = [:]
kkonganti@105 6 Map toolspecs = [:]
kkonganti@105 7 tool.text = [:]
kkonganti@105 8 tool.helpparams = [:]
kkonganti@105 9
kkonganti@105 10 toolspecs = [
kkonganti@105 11 'flye_pacbio_raw': [
kkonganti@105 12 clihelp: 'Input FASTQ reads are PacBio regular CLR reads (<20% error) ' +
kkonganti@105 13 "Defaut: ${params.flye_pacbio_raw}",
kkonganti@105 14 cliflag: '--pacbio-raw',
kkonganti@105 15 clivalue: (params.flye_pacbio_raw ? ' ' : '')
kkonganti@105 16 ],
kkonganti@105 17 'flye_pacbio_corr': [
kkonganti@105 18 clihelp: 'Input FASTQ reads are PacBio reads that were corrected ' +
kkonganti@105 19 "with other methods (<3% error). Default: ${params.flye_pacbio_corr}",
kkonganti@105 20 cliflag: '--pacbio-corr',
kkonganti@105 21 clivalue: (params.flye_pacbio_corr ? ' ' : '')
kkonganti@105 22 ],
kkonganti@105 23 'flye_pacbio_hifi': [
kkonganti@105 24 clihelp: 'Input FASTQ reads are PacBio HiFi reads (<1% error). ' +
kkonganti@105 25 "Default: ${params.flye_pacbio_hifi}",
kkonganti@105 26 cliflag: '--pacbio-hifi',
kkonganti@105 27 clivalue: (params.flye_pacbio_hifi ? ' ' : '')
kkonganti@105 28 ],
kkonganti@105 29 'flye_nano_raw': [
kkonganti@105 30 clihelp: 'Input FASTQ reads are ONT regular reads, pre-Guppy5 (<20% error). ' +
kkonganti@105 31 "Default: ${params.flye_nano_raw}",
kkonganti@105 32 cliflag: '--nano-raw',
kkonganti@105 33 clivalue: (params.flye_nano_raw ? ' ' : '')
kkonganti@105 34 ],
kkonganti@105 35 'flye_nano_corr': [
kkonganti@105 36 clihelp: 'Input FASTQ reads are ONT reads that were corrected with other ' +
kkonganti@105 37 "methods (<3% error). Default: ${params.flye_nano_corr}",
kkonganti@105 38 cliflag: '--nano-corr',
kkonganti@105 39 clivalue: (params.flye_nano_corr ? ' ' : '')
kkonganti@105 40 ],
kkonganti@105 41 'flye_nano_hq': [
kkonganti@105 42 clihelp: 'Input FASTQ reads are ONT high-quality reads: ' +
kkonganti@105 43 "Guppy5+ SUP or Q20 (<5% error). Default: ${params.flye_nano_hq}",
kkonganti@105 44 cliflag: '--nano-hq',
kkonganti@105 45 clivalue: (params.flye_nano_hq ? ' ' : '')
kkonganti@105 46 ],
kkonganti@105 47 'flye_genome_size': [
kkonganti@105 48 clihelp: 'Estimated genome size (for example, 5m or 2.6g). ' +
kkonganti@105 49 "Default: ${params.flye_genome_size}",
kkonganti@105 50 cliflag: '--genome-size',
kkonganti@105 51 clivalue: (params.flye_genome_size ?: '')
kkonganti@105 52 ],
kkonganti@105 53 'flye_polish_iter': [
kkonganti@105 54 clihelp: 'Number of genome polishing iterations. ' +
kkonganti@105 55 "Default: ${params.flye_polish_iter}",
kkonganti@105 56 cliflag: '--iterations',
kkonganti@105 57 clivalue: (params.flye_polish_iter ?: '')
kkonganti@105 58 ],
kkonganti@105 59 'flye_meta': [
kkonganti@105 60 clihelp: "Do a metagenome assembly (unenven coverage mode). Default: ${params.flye_meta}",
kkonganti@105 61 cliflag: '--meta',
kkonganti@105 62 clivalue: (params.flye_meta ? ' ' : '')
kkonganti@105 63 ],
kkonganti@105 64 'flye_min_overlap': [
kkonganti@105 65 clihelp: "Minimum overlap between reads. Default: ${params.flye_min_overlap}",
kkonganti@105 66 cliflag: '--min-overlap',
kkonganti@105 67 clivalue: (params.flye_min_overlap ?: '')
kkonganti@105 68 ],
kkonganti@105 69 'flye_scaffold': [
kkonganti@105 70 clihelp: "Enable scaffolding using assembly graph. Default: ${params.flye_scaffold}",
kkonganti@105 71 cliflag: '--scaffold',
kkonganti@105 72 clivalue: (params.flye_scaffold ? ' ' : '')
kkonganti@105 73 ]
kkonganti@105 74 ]
kkonganti@105 75
kkonganti@105 76 toolspecs.each {
kkonganti@105 77 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@105 78 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@105 79 }
kkonganti@105 80
kkonganti@105 81 return tool
kkonganti@105 82 }