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1 workflow Resistance {
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2 File inputSamplesFile
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3 Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
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4
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5 String outputDir
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6 Float geneCov
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7 Float geneID
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8 Float pointCov
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9 Float pointID
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10 String python
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11 String kma
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12 String blastn
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13 String resfinder
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14 String resDB
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15 String pointDB
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16
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17 scatter (sample in inputSamples) {
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18 call ResFinder {
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19 input: inputSample=sample,
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20 outputRoot=outputDir,
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21 geneCov=geneCov,
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22 geneID=geneID,
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23 pointCov=pointCov,
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24 pointID=pointID,
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25 python=python,
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26 kma=kma,
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27 blastn=blastn,
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28 resfinder=resfinder,
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29 resDB=resDB,
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30 pointDB=pointDB
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31 }
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32 }
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33 }
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34
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35 task ResFinder {
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36
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37 Array[String] inputSample
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38 Float geneCov
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39 Float geneID
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40 Float pointCov
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41 Float pointID
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42 String python
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43 String kma
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44 String blastn
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45 String resfinder
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46 String resDB
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47 String pointDB
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48
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49 String inputPath1 = inputSample[0]
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50 String inputPath2 = inputSample[1]
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51 String species = inputSample[2]
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52 String inputType = inputSample[3]
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53
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54 String outputRoot
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55 String filename = basename(inputPath1)
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56 String out_dir_name = "${outputRoot}/${filename}.rf_out"
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57
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58 command {
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59
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60 set +u
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61 module unload mgmapper metabat fastqc
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62 module unload ncbi-blast perl
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63 source /home/projects/cge/apps/env/rf4_env/bin/activate
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64 module load perl
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65 module load ncbi-blast/2.8.1+
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66
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67 mkdir ${out_dir_name}
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68
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69 inputArgs=""
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70 pointArgs=""
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71
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72 if [ "${species}" = "other" ] && [ "${inputType}" = "paired" ]
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73 then
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74 inputArgs+="-ifq ${inputPath1} ${inputPath2}"
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75 elif [ "${inputType}" = "paired" ]
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76 then
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77 inputArgs+="-ifq ${inputPath1} ${inputPath2}"
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78 pointArgs+="--point --db_path_point ${pointDB} --min_cov_point ${pointCov} --threshold_point ${pointID}"
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79 elif [ "${species}" = "other"] && [ "${inputType}" = "assembly" ]
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80 then
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81 inputArgs+="-ifa ${inputPath1}"
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82 elif [ "${inputType}" = "assembly" ]
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83 then
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84 inputArgs+="-ifa ${inputPath1}"
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85 pointArgs+="--point --db_path_point ${pointDB} --min_cov_point ${pointCov} --threshold_point ${pointID}"
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86 fi
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87
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88 ${python} ${resfinder} \
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89 $inputArgs \
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90 --blastPath ${blastn} \
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91 --kmaPath ${kma} \
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92 --species "${species}" \
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93 --db_path_res ${resDB} \
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94 --acquired \
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95 --acq_overlap 30 \
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96 --min_cov ${geneCov} \
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97 --threshold ${geneID} \
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98 -o ${out_dir_name} \
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99 $pointArgs
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100 }
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101 output {
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102 File rf_out = "${out_dir_name}/std_format_under_development.json"
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103 }
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104 runtime {
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105 walltime: "1:00:00"
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106 cpu: 2
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107 memory: "4 GB"
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108 queue: "cge"
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109 }
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110 }
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