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annotate 0.4.2/lib/help/spades.nf @ 130:04f6ac8ca13c

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author kkonganti
date Wed, 03 Jul 2024 15:16:39 -0400
parents 52045ea4679d
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kkonganti@105 1 // Help text for spades within CPIPES.
kkonganti@105 2
kkonganti@105 3 def spadesHelp(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 'spades_run': [
kkonganti@105 12 clihelp: 'Run SPAdes assembler. Default: ' +
kkonganti@105 13 (params.spades_run ?: false),
kkonganti@105 14 cliflag: null,
kkonganti@105 15 clivalue: null
kkonganti@105 16 ],
kkonganti@105 17 'spades_isolate': [
kkonganti@105 18 clihelp: 'This flag is highly recommended for high-coverage isolate and ' +
kkonganti@105 19 "multi-cell data. Defaut: ${params.spades_isolate}",
kkonganti@105 20 cliflag: '--isolate',
kkonganti@105 21 clivalue: (params.spades_isolate ? ' ' : '')
kkonganti@105 22 ],
kkonganti@105 23 'spades_sc': [
kkonganti@105 24 clihelp: 'This flag is required for MDA (single-cell) data. ' +
kkonganti@105 25 "Default: ${params.spades_sc}",
kkonganti@105 26 cliflag: '--sc',
kkonganti@105 27 clivalue: (params.spades_sc ? ' ' : '')
kkonganti@105 28 ],
kkonganti@105 29 'spades_meta': [
kkonganti@105 30 clihelp: 'This flag is required for metagenomic data. ' +
kkonganti@105 31 "Default: ${params.spades_meta}",
kkonganti@105 32 cliflag: '--meta',
kkonganti@105 33 clivalue: (params.spades_meta ? ' ' : '')
kkonganti@105 34 ],
kkonganti@105 35 'spades_bio': [
kkonganti@105 36 clihelp: 'This flag is required for biosytheticSPAdes mode. ' +
kkonganti@105 37 "Default: ${params.spades_bio}",
kkonganti@105 38 cliflag: '--bio',
kkonganti@105 39 clivalue: (params.spades_bio ? ' ' : '')
kkonganti@105 40 ],
kkonganti@105 41 'spades_corona': [
kkonganti@105 42 clihelp: 'This flag is required for coronaSPAdes mode. ' +
kkonganti@105 43 "Default: ${params.spades_corona}",
kkonganti@105 44 cliflag: '--corona',
kkonganti@105 45 clivalue: (params.spades_corona ? ' ' : '')
kkonganti@105 46 ],
kkonganti@105 47 'spades_rna': [
kkonganti@105 48 clihelp: 'This flag is required for RNA-Seq data. ' +
kkonganti@105 49 "Default: ${params.spades_rna}",
kkonganti@105 50 cliflag: '--rna',
kkonganti@105 51 clivalue: (params.spades_rna ? ' ' : '')
kkonganti@105 52 ],
kkonganti@105 53 'spades_plasmid': [
kkonganti@105 54 clihelp: 'Runs plasmidSPAdes pipeline for plasmid detection. ' +
kkonganti@105 55 "Default: ${params.spades_plasmid}",
kkonganti@105 56 cliflag: '--plasmid',
kkonganti@105 57 clivalue: (params.spades_plasmid ? ' ' : '')
kkonganti@105 58 ],
kkonganti@105 59 'spades_metaviral': [
kkonganti@105 60 clihelp: 'Runs metaviralSPAdes pipeline for virus detection. ' +
kkonganti@105 61 "Default: ${params.spades_metaviral}",
kkonganti@105 62 cliflag: '--metaviral',
kkonganti@105 63 clivalue: (params.spades_metaviral ? ' ' : '')
kkonganti@105 64 ],
kkonganti@105 65 'spades_metaplasmid': [
kkonganti@105 66 clihelp: 'Runs metaplasmidSPAdes pipeline for plasmid detection in ' +
kkonganti@105 67 "metagenomics datasets. Default: ${params.spades_metaplasmid}",
kkonganti@105 68 cliflag: '--metaplasmid',
kkonganti@105 69 clivalue: (params.spades_metaplasmid ? ' ' : '')
kkonganti@105 70 ],
kkonganti@105 71 'spades_rnaviral': [
kkonganti@105 72 clihelp: 'This flag enables virus assembly module from RNA-Seq data. ' +
kkonganti@105 73 "Default: ${params.spades_rnaviral}",
kkonganti@105 74 cliflag: '--rnaviral',
kkonganti@105 75 clivalue: (params.spades_rnaviral ? ' ' : '')
kkonganti@105 76 ],
kkonganti@105 77 'spades_iontorrent': [
kkonganti@105 78 clihelp: 'This flag is required for IonTorrent data. ' +
kkonganti@105 79 "Default: ${params.spades_iontorrent}",
kkonganti@105 80 cliflag: '--iontorrent',
kkonganti@105 81 clivalue: (params.spades_iontorrent ? ' ' : '')
kkonganti@105 82 ],
kkonganti@105 83 'spades_only_assembler': [
kkonganti@105 84 clihelp: 'Runs only the SPAdes assembler module (without read error correction). ' +
kkonganti@105 85 "Default: ${params.spades_only_assembler}",
kkonganti@105 86 cliflag: '--only-assembler',
kkonganti@105 87 clivalue: (params.spades_only_assembler ? ' ' : '')
kkonganti@105 88 ],
kkonganti@105 89 'spades_careful': [
kkonganti@105 90 clihelp: 'Tries to reduce the number of mismatches and short indels in the assembly. ' +
kkonganti@105 91 "Default: ${params.spades_careful}",
kkonganti@105 92 cliflag: '--careful',
kkonganti@105 93 clivalue: (params.spades_careful ? ' ' : '')
kkonganti@105 94 ],
kkonganti@105 95 'spades_cov_cutoff': [
kkonganti@105 96 clihelp: 'Coverage cutoff value (a positive float number). ' +
kkonganti@105 97 "Default: ${params.spades_cov_cutoff}",
kkonganti@105 98 cliflag: '--cov-cutoff',
kkonganti@105 99 clivalue: (params.spades_cov_cutoff ?: '')
kkonganti@105 100 ],
kkonganti@105 101 'spades_k': [
kkonganti@105 102 clihelp: 'List of k-mer sizes (must be odd and less than 128). ' +
kkonganti@105 103 "Default: ${params.spades_k}",
kkonganti@105 104 cliflag: '-k',
kkonganti@105 105 clivalue: (params.spades_k ?: '')
kkonganti@105 106 ],
kkonganti@105 107 'spades_hmm': [
kkonganti@105 108 clihelp: 'Directory with custom hmms that replace the default ones (very rare). ' +
kkonganti@105 109 "Default: ${params.spades_hmm}",
kkonganti@105 110 cliflag: '--custom-hmms',
kkonganti@105 111 clivalue: (params.spades_hmm ?: '')
kkonganti@105 112 ]
kkonganti@105 113 ]
kkonganti@105 114
kkonganti@105 115 toolspecs.each {
kkonganti@105 116 k, v -> tool.text['--' + k] = "${v.clihelp}"
kkonganti@105 117 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
kkonganti@105 118 }
kkonganti@105 119
kkonganti@105 120 return tool
kkonganti@105 121 }