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