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annotate 0.7.0/lib/help/flye.nf @ 21:4ce0e079377d tip

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author kkonganti
date Mon, 15 Jul 2024 12:01:00 -0400
parents 0e7a0053e4a6
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kkonganti@17 1 // Help text for flye within CPIPES.
kkonganti@17 2
kkonganti@17 3 def flyeHelp(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 'flye_pacbio_raw': [
kkonganti@17 12 clihelp: 'Input FASTQ reads are PacBio regular CLR reads (<20% error) ' +
kkonganti@17 13 "Default: ${params.flye_pacbio_raw}",
kkonganti@17 14 cliflag: '--pacbio-raw',
kkonganti@17 15 clivalue: (params.flye_pacbio_raw ? ' ' : '')
kkonganti@17 16 ],
kkonganti@17 17 'flye_pacbio_corr': [
kkonganti@17 18 clihelp: 'Input FASTQ reads are PacBio reads that were corrected ' +
kkonganti@17 19 "with other methods (<3% error). Default: ${params.flye_pacbio_corr}",
kkonganti@17 20 cliflag: '--pacbio-corr',
kkonganti@17 21 clivalue: (params.flye_pacbio_corr ? ' ' : '')
kkonganti@17 22 ],
kkonganti@17 23 'flye_pacbio_hifi': [
kkonganti@17 24 clihelp: 'Input FASTQ reads are PacBio HiFi reads (<1% error). ' +
kkonganti@17 25 "Default: ${params.flye_pacbio_hifi}",
kkonganti@17 26 cliflag: '--pacbio-hifi',
kkonganti@17 27 clivalue: (params.flye_pacbio_hifi ? ' ' : '')
kkonganti@17 28 ],
kkonganti@17 29 'flye_nano_raw': [
kkonganti@17 30 clihelp: 'Input FASTQ reads are ONT regular reads, pre-Guppy5 (<20% error). ' +
kkonganti@17 31 "Default: ${params.flye_nano_raw}",
kkonganti@17 32 cliflag: '--nano-raw',
kkonganti@17 33 clivalue: (params.flye_nano_raw ? ' ' : '')
kkonganti@17 34 ],
kkonganti@17 35 'flye_nano_corr': [
kkonganti@17 36 clihelp: 'Input FASTQ reads are ONT reads that were corrected with other ' +
kkonganti@17 37 "methods (<3% error). Default: ${params.flye_nano_corr}",
kkonganti@17 38 cliflag: '--nano-corr',
kkonganti@17 39 clivalue: (params.flye_nano_corr ? ' ' : '')
kkonganti@17 40 ],
kkonganti@17 41 'flye_nano_hq': [
kkonganti@17 42 clihelp: 'Input FASTQ reads are ONT high-quality reads: ' +
kkonganti@17 43 "Guppy5+ SUP or Q20 (<5% error). Default: ${params.flye_nano_hq}",
kkonganti@17 44 cliflag: '--nano-hq',
kkonganti@17 45 clivalue: (params.flye_nano_hq ? ' ' : '')
kkonganti@17 46 ],
kkonganti@17 47 'flye_genome_size': [
kkonganti@17 48 clihelp: 'Estimated genome size (for example, 5m or 2.6g). ' +
kkonganti@17 49 "Default: ${params.flye_genome_size}",
kkonganti@17 50 cliflag: '--genome-size',
kkonganti@17 51 clivalue: (params.flye_genome_size ?: '')
kkonganti@17 52 ],
kkonganti@17 53 'flye_polish_iter': [
kkonganti@17 54 clihelp: 'Number of genome polishing iterations. ' +
kkonganti@17 55 "Default: ${params.flye_polish_iter}",
kkonganti@17 56 cliflag: '--iterations',
kkonganti@17 57 clivalue: (params.flye_polish_iter ?: '')
kkonganti@17 58 ],
kkonganti@17 59 'flye_meta': [
kkonganti@17 60 clihelp: "Do a metagenome assembly (unenven coverage mode). Default: ${params.flye_meta}",
kkonganti@17 61 cliflag: '--meta',
kkonganti@17 62 clivalue: (params.flye_meta ? ' ' : '')
kkonganti@17 63 ],
kkonganti@17 64 'flye_min_overlap': [
kkonganti@17 65 clihelp: "Minimum overlap between reads. Default: ${params.flye_min_overlap}",
kkonganti@17 66 cliflag: '--min-overlap',
kkonganti@17 67 clivalue: (params.flye_min_overlap ?: '')
kkonganti@17 68 ],
kkonganti@17 69 'flye_scaffold': [
kkonganti@17 70 clihelp: "Enable scaffolding using assembly graph. Default: ${params.flye_scaffold}",
kkonganti@17 71 cliflag: '--scaffold',
kkonganti@17 72 clivalue: (params.flye_scaffold ? ' ' : '')
kkonganti@17 73 ]
kkonganti@17 74 ]
kkonganti@17 75
kkonganti@17 76 toolspecs.each {
kkonganti@17 77 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17 78 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17 79 }
kkonganti@17 80
kkonganti@17 81 return tool
kkonganti@17 82 }