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1 // Help text for spades within CPIPES.
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2
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3 def spadesHelp(params) {
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4
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5 Map tool = [:]
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6 Map toolspecs = [:]
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7 tool.text = [:]
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8 tool.helpparams = [:]
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9
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10 toolspecs = [
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11 'spades_run': [
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12 clihelp: 'Run SPAdes assembler. Default: ' +
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13 (params.spades_run ?: false),
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14 cliflag: null,
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15 clivalue: null
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16 ],
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17 'spades_isolate': [
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18 clihelp: 'This flag is highly recommended for high-coverage isolate and ' +
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19 "multi-cell data. Defaut: ${params.spades_isolate}",
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20 cliflag: '--isolate',
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21 clivalue: (params.spades_isolate ? ' ' : '')
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22 ],
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23 'spades_sc': [
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24 clihelp: 'This flag is required for MDA (single-cell) data. ' +
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25 "Default: ${params.spades_sc}",
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26 cliflag: '--sc',
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27 clivalue: (params.spades_sc ? ' ' : '')
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28 ],
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29 'spades_meta': [
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30 clihelp: 'This flag is required for metagenomic data. ' +
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31 "Default: ${params.spades_meta}",
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32 cliflag: '--meta',
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33 clivalue: (params.spades_meta ? ' ' : '')
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34 ],
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35 'spades_bio': [
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36 clihelp: 'This flag is required for biosytheticSPAdes mode. ' +
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37 "Default: ${params.spades_bio}",
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38 cliflag: '--bio',
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39 clivalue: (params.spades_bio ? ' ' : '')
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40 ],
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41 'spades_corona': [
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42 clihelp: 'This flag is required for coronaSPAdes mode. ' +
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43 "Default: ${params.spades_corona}",
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44 cliflag: '--corona',
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45 clivalue: (params.spades_corona ? ' ' : '')
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46 ],
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47 'spades_rna': [
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48 clihelp: 'This flag is required for RNA-Seq data. ' +
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49 "Default: ${params.spades_rna}",
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50 cliflag: '--rna',
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51 clivalue: (params.spades_rna ? ' ' : '')
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52 ],
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53 'spades_plasmid': [
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54 clihelp: 'Runs plasmidSPAdes pipeline for plasmid detection. ' +
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55 "Default: ${params.spades_plasmid}",
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56 cliflag: '--plasmid',
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57 clivalue: (params.spades_plasmid ? ' ' : '')
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58 ],
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59 'spades_metaviral': [
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60 clihelp: 'Runs metaviralSPAdes pipeline for virus detection. ' +
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61 "Default: ${params.spades_metaviral}",
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62 cliflag: '--metaviral',
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63 clivalue: (params.spades_metaviral ? ' ' : '')
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64 ],
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65 'spades_metaplasmid': [
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66 clihelp: 'Runs metaplasmidSPAdes pipeline for plasmid detection in ' +
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67 "metagenomics datasets. Default: ${params.spades_metaplasmid}",
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68 cliflag: '--metaplasmid',
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69 clivalue: (params.spades_metaplasmid ? ' ' : '')
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70 ],
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71 'spades_rnaviral': [
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72 clihelp: 'This flag enables virus assembly module from RNA-Seq data. ' +
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73 "Default: ${params.spades_rnaviral}",
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74 cliflag: '--rnaviral',
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75 clivalue: (params.spades_rnaviral ? ' ' : '')
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76 ],
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77 'spades_iontorrent': [
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78 clihelp: 'This flag is required for IonTorrent data. ' +
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79 "Default: ${params.spades_iontorrent}",
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80 cliflag: '--iontorrent',
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81 clivalue: (params.spades_iontorrent ? ' ' : '')
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82 ],
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83 'spades_only_assembler': [
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84 clihelp: 'Runs only the SPAdes assembler module (without read error correction). ' +
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85 "Default: ${params.spades_only_assembler}",
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86 cliflag: '--only-assembler',
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87 clivalue: (params.spades_only_assembler ? ' ' : '')
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88 ],
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89 'spades_careful': [
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90 clihelp: 'Tries to reduce the number of mismatches and short indels in the assembly. ' +
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91 "Default: ${params.spades_careful}",
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92 cliflag: '--careful',
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93 clivalue: (params.spades_careful ? ' ' : '')
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94 ],
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95 'spades_cov_cutoff': [
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96 clihelp: 'Coverage cutoff value (a positive float number). ' +
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97 "Default: ${params.spades_cov_cutoff}",
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98 cliflag: '--cov-cutoff',
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99 clivalue: (params.spades_cov_cutoff ?: '')
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100 ],
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101 'spades_k': [
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102 clihelp: 'List of k-mer sizes (must be odd and less than 128). ' +
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103 "Default: ${params.spades_k}",
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104 cliflag: '-k',
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105 clivalue: (params.spades_k ?: '')
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106 ],
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107 'spades_hmm': [
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108 clihelp: 'Directory with custom hmms that replace the default ones (very rare). ' +
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109 "Default: ${params.spades_hmm}",
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110 cliflag: '--custom-hmms',
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111 clivalue: (params.spades_hmm ?: '')
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112 ]
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113 ]
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114
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115 toolspecs.each {
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116 k, v -> tool.text['--' + k] = "${v.clihelp}"
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117 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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118 }
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119
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120 return tool
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121 } |
