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annotate 0.7.0/lib/help/spades.nf @ 18:75558ffe3e68

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author kkonganti
date Mon, 15 Jul 2024 11:01:13 -0400
parents 0e7a0053e4a6
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kkonganti@17 1 // Help text for spades within CPIPES.
kkonganti@17 2
kkonganti@17 3 def spadesHelp(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 'spades_run': [
kkonganti@17 12 clihelp: 'Run SPAdes assembler. Default: ' +
kkonganti@17 13 (params.spades_run ?: false),
kkonganti@17 14 cliflag: null,
kkonganti@17 15 clivalue: null
kkonganti@17 16 ],
kkonganti@17 17 'spades_isolate': [
kkonganti@17 18 clihelp: 'This flag is highly recommended for high-coverage isolate and ' +
kkonganti@17 19 "multi-cell data. Default: ${params.spades_isolate}",
kkonganti@17 20 cliflag: '--isolate',
kkonganti@17 21 clivalue: (params.spades_isolate ? ' ' : '')
kkonganti@17 22 ],
kkonganti@17 23 'spades_sc': [
kkonganti@17 24 clihelp: 'This flag is required for MDA (single-cell) data. ' +
kkonganti@17 25 "Default: ${params.spades_sc}",
kkonganti@17 26 cliflag: '--sc',
kkonganti@17 27 clivalue: (params.spades_sc ? ' ' : '')
kkonganti@17 28 ],
kkonganti@17 29 'spades_meta': [
kkonganti@17 30 clihelp: 'This flag is required for metagenomic data. ' +
kkonganti@17 31 "Default: ${params.spades_meta}",
kkonganti@17 32 cliflag: '--meta',
kkonganti@17 33 clivalue: (params.spades_meta ? ' ' : '')
kkonganti@17 34 ],
kkonganti@17 35 'spades_bio': [
kkonganti@17 36 clihelp: 'This flag is required for biosytheticSPAdes mode. ' +
kkonganti@17 37 "Default: ${params.spades_bio}",
kkonganti@17 38 cliflag: '--bio',
kkonganti@17 39 clivalue: (params.spades_bio ? ' ' : '')
kkonganti@17 40 ],
kkonganti@17 41 'spades_corona': [
kkonganti@17 42 clihelp: 'This flag is required for coronaSPAdes mode. ' +
kkonganti@17 43 "Default: ${params.spades_corona}",
kkonganti@17 44 cliflag: '--corona',
kkonganti@17 45 clivalue: (params.spades_corona ? ' ' : '')
kkonganti@17 46 ],
kkonganti@17 47 'spades_rna': [
kkonganti@17 48 clihelp: 'This flag is required for RNA-Seq data. ' +
kkonganti@17 49 "Default: ${params.spades_rna}",
kkonganti@17 50 cliflag: '--rna',
kkonganti@17 51 clivalue: (params.spades_rna ? ' ' : '')
kkonganti@17 52 ],
kkonganti@17 53 'spades_plasmid': [
kkonganti@17 54 clihelp: 'Runs plasmidSPAdes pipeline for plasmid detection. ' +
kkonganti@17 55 "Default: ${params.spades_plasmid}",
kkonganti@17 56 cliflag: '--plasmid',
kkonganti@17 57 clivalue: (params.spades_plasmid ? ' ' : '')
kkonganti@17 58 ],
kkonganti@17 59 'spades_metaviral': [
kkonganti@17 60 clihelp: 'Runs metaviralSPAdes pipeline for virus detection. ' +
kkonganti@17 61 "Default: ${params.spades_metaviral}",
kkonganti@17 62 cliflag: '--metaviral',
kkonganti@17 63 clivalue: (params.spades_metaviral ? ' ' : '')
kkonganti@17 64 ],
kkonganti@17 65 'spades_metaplasmid': [
kkonganti@17 66 clihelp: 'Runs metaplasmidSPAdes pipeline for plasmid detection in ' +
kkonganti@17 67 "metagenomics datasets. Default: ${params.spades_metaplasmid}",
kkonganti@17 68 cliflag: '--metaplasmid',
kkonganti@17 69 clivalue: (params.spades_metaplasmid ? ' ' : '')
kkonganti@17 70 ],
kkonganti@17 71 'spades_rnaviral': [
kkonganti@17 72 clihelp: 'This flag enables virus assembly module from RNA-Seq data. ' +
kkonganti@17 73 "Default: ${params.spades_rnaviral}",
kkonganti@17 74 cliflag: '--rnaviral',
kkonganti@17 75 clivalue: (params.spades_rnaviral ? ' ' : '')
kkonganti@17 76 ],
kkonganti@17 77 'spades_iontorrent': [
kkonganti@17 78 clihelp: 'This flag is required for IonTorrent data. ' +
kkonganti@17 79 "Default: ${params.spades_iontorrent}",
kkonganti@17 80 cliflag: '--iontorrent',
kkonganti@17 81 clivalue: (params.spades_iontorrent ? ' ' : '')
kkonganti@17 82 ],
kkonganti@17 83 'spades_only_assembler': [
kkonganti@17 84 clihelp: 'Runs only the SPAdes assembler module (without read error correction). ' +
kkonganti@17 85 "Default: ${params.spades_only_assembler}",
kkonganti@17 86 cliflag: '--only-assembler',
kkonganti@17 87 clivalue: (params.spades_only_assembler ? ' ' : '')
kkonganti@17 88 ],
kkonganti@17 89 'spades_careful': [
kkonganti@17 90 clihelp: 'Tries to reduce the number of mismatches and short indels in the assembly. ' +
kkonganti@17 91 "Default: ${params.spades_careful}",
kkonganti@17 92 cliflag: '--careful',
kkonganti@17 93 clivalue: (params.spades_careful ? ' ' : '')
kkonganti@17 94 ],
kkonganti@17 95 'spades_cov_cutoff': [
kkonganti@17 96 clihelp: 'Coverage cutoff value (a positive float number). ' +
kkonganti@17 97 "Default: ${params.spades_cov_cutoff}",
kkonganti@17 98 cliflag: '--cov-cutoff',
kkonganti@17 99 clivalue: (params.spades_cov_cutoff ?: '')
kkonganti@17 100 ],
kkonganti@17 101 'spades_k': [
kkonganti@17 102 clihelp: 'List of k-mer sizes (must be odd and less than 128). ' +
kkonganti@17 103 "Default: ${params.spades_k}",
kkonganti@17 104 cliflag: '-k',
kkonganti@17 105 clivalue: (params.spades_k ?: '')
kkonganti@17 106 ],
kkonganti@17 107 'spades_hmm': [
kkonganti@17 108 clihelp: 'Directory with custom hmms that replace the default ones (very rare). ' +
kkonganti@17 109 "Default: ${params.spades_hmm}",
kkonganti@17 110 cliflag: '--custom-hmms',
kkonganti@17 111 clivalue: (params.spades_hmm ?: '')
kkonganti@17 112 ]
kkonganti@17 113 ]
kkonganti@17 114
kkonganti@17 115 toolspecs.each {
kkonganti@17 116 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@17 117 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@17 118 }
kkonganti@17 119
kkonganti@17 120 return tool
kkonganti@17 121 }