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1 // Help text for salmon index within CPIPES.
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2
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3 def salmonidxHelp(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 'salmonidx_run': [
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12 clihelp: 'Run `salmon index` tool. Default: ' +
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13 (params.salmonidx_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 'salmonidx_k': [
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18 clihelp: 'The size of k-mers that should be used for the ' +
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19 " quasi index. Default: ${params.salmonidx_k}",
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20 cliflag: '-k',
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21 clivalue: (params.salmonidx_k ?: '')
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22 ],
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23 'salmonidx_gencode': [
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24 clihelp: 'This flag will expect the input transcript FASTA ' +
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25 'to be in GENCODE format, and will split the transcript ' +
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26 'name at the first `|` character. These reduced names ' +
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27 'will be used in the output and when looking for these ' +
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28 'transcripts in a gene to transcript GTF.' +
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29 " Default: ${params.salmonidx_gencode}",
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30 cliflag: '--gencode',
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31 clivalue: (params.salmonidx_gencode ? ' ' : '')
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32 ],
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33 'salmonidx_features': [
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34 clihelp: 'This flag will expect the input reference to be in the ' +
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35 'tsv file format, and will split the feature name at the first ' +
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36 '`tab` character. These reduced names will be used in the output ' +
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37 'and when looking for the sequence of the features. GTF.' +
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38 " Default: ${params.salmonidx_features}",
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39 cliflag: '--features',
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40 clivalue: (params.salmonidx_features ? ' ' : '')
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41 ],
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42 'salmonidx_keepDuplicates': [
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43 clihelp: 'This flag will disable the default indexing behavior of ' +
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44 'discarding sequence-identical duplicate transcripts. If this ' +
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45 'flag is passed then duplicate transcripts that appear in the ' +
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46 'input will be retained and quantified separately.' +
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47 " Default: ${params.salmonidx_keepDuplicates}",
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48 cliflag: '--keepDuplicates',
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49 clivalue: (params.salmonidx_keepDuplicates ? ' ' : '')
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50 ],
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51 'salmonidx_keepFixedFasta': [
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52 clihelp: 'Retain the fixed fasta file (without short ' +
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53 'transcripts and duplicates, clipped, etc.) generated ' +
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54 "during indexing. Default: ${params.salmonidx_keepFixedFasta}",
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55 cliflag: '--keepFixedFasta',
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56 clivalue: (params.salmonidx_keepFixedFasta ?: '')
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57 ],
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58 'salmonidx_filterSize': [
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59 clihelp: 'The size of the Bloom filter that will be used ' +
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60 'by TwoPaCo during indexing. The filter will be of ' +
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61 'size 2^{filterSize}. A value of -1 means that the ' +
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62 'filter size will be automatically set based on the ' +
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63 'number of distinct k-mers in the input, as estimated by ' +
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64 "nthll. Default: ${params.salmonidx_filterSize}",
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65 cliflag: '--filterSize',
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66 clivalue: (params.salmonidx_filterSize ?: '')
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67 ],
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68 'salmonidx_sparse': [
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69 clihelp: 'Build the index using a sparse sampling of k-mer ' +
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70 'positions This will require less memory (especially ' +
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71 'during quantification), but will take longer to construct' +
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72 'and can slow down mapping / alignment.' +
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73 " Default: ${params.salmonidx_sparse}",
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74 cliflag: '--sparse',
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75 clivalue: (params.salmonidx_sparse ? ' ' : '')
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76 ],
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77 'salmonidx_n': [
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78 clihelp: 'Do not clip poly-A tails from the ends of target ' +
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79 "sequences. Default: ${params.salmonidx_n}",
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80 cliflag: '-n',
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81 clivalue: (params.salmonidx_n ? ' ' : '')
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82 ]
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83 ]
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84
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85 toolspecs.each {
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86 k, v -> tool.text['--' + k] = "${v.clihelp}"
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87 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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88 }
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89
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90 return tool
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91 } |
