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rliterman@0
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1 // Subworkflow to run RefChooser for list of queries
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2
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3 // Set directory structure
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4 output_directory = file(params.output_directory)
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5 log_directory = file(params.log_directory)
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6 mash_directory = file(params.mash_directory)
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7
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8 workflow {
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9 main:
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10 // Run RefChooser
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11 reference_data = runRefChooser(query_data: query_data)
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12 publish:
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13 // Publish reference data
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14 reference_data >> 'reference.fa'
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15 }
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16
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17 workflow runRefChooser{
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18 take:
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19 query_data
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20
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21 emit:
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22 reference_data
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23
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24 main:
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25
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26 // Make MASH sketches (1 CPU per query) and generate triangle (all CPUs)
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27 mash_refs = query_data
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28 .unique{it -> it[1]}
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29 .map { [ it[0], it[1] ] }
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30 | mashSketch
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31 | collect
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32 | mashTriangle
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33 | chooseRefs
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34 | splitCsv | collect | flatten | collate(1)
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35
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36 reference_data = query_data
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37 .map{it -> tuple(it[1].toString(),it[0])}
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38 .join(mash_refs, by:0)
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39 .map{tuple(it[1],it[0])}
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40 .unique{it -> it[0]}.collect().flatten().collate(2)
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41
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42 // Save reference data to file
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43 reference_data
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44 .collect{it -> it[0]}
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45 | saveRefIDs
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46 }
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47
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48 process chooseRefs{
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49
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50 executor = 'local'
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51 cpus = 1
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52 maxForks = 1
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53
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54 input:
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55 val(mash_triangle)
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56
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57 output:
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58 stdout
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59
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60 script:
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61
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62 ref_count = params.n_ref.toInteger()
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63 ref_script = file("${projectDir}/bin/chooseRefs.py")
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64 """
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65 $params.load_python_module
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66 cd $mash_directory
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67
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68 python $ref_script --ref_count $ref_count --mash_triangle_file $mash_triangle --trim_name "${params.trim_name}"
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69 """
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70 }
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71
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72 process mashTriangle{
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73
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74 input:
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75 val(mash_sketches)
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76
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77 output:
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78 stdout
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79
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80 script:
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81
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82 sketch_file = file("${mash_directory}/Mash_Sketches.txt")
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83 mash_triangle_file = file("${mash_directory}/Mash_Triangle")
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84
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85 """
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86 $params.load_mash_module
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87 ls ${mash_directory}/*.msh > $sketch_file
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88 mash triangle -p ${params.cores} -l $sketch_file > $mash_triangle_file
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89 echo -n $mash_triangle_file
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90 """
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91 }
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92
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93 process mashSketch{
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94 cpus = 1
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95
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96 input:
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97 tuple val(query_name),val(query_fasta)
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98
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99 output:
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100 stdout
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101
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102 script:
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103
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104 mash_path = "${mash_directory}/${query_name}.msh"
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105 """
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106 $params.load_mash_module
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107 mash sketch -s 10000 -p 1 -o $mash_path $query_fasta
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108 echo -n "${mash_path}"
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109 """
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110 }
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111
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112 process saveRefIDs{
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113 executor = 'local'
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114 cpus = 1
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115 maxForks = 1
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116
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117 input:
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118 val(ref_ids)
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119
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120 script:
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121 ref_id_file = file(params.ref_id_file)
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122 ref_id_file.append(ref_ids.join('\n') + '\n')
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123 """
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124 """
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125 }
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