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1 // Define any required imports for this specific workflow
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2 import java.nio.file.Paths
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3 import nextflow.file.FileHelper
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4
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5 // Include any necessary methods
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6 include { \
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7 summaryOfParams; stopNow; fastqEntryPointHelp; sendMail; \
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8 addPadding; wrapUpHelp } from "${params.routines}"
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9 include { spadesHelp } from "${params.toolshelp}${params.fs}spades"
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10
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11
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12 // Exit if help requested before any subworkflows
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13 if (params.help) {
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14 log.info help()
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15 exit 0
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16 }
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17
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18 // Include any necessary modules and subworkflows
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19 include { PROCESS_FASTQ } from "${params.subworkflows}${params.fs}process_fastq"
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20 include { SPADES_ASSEMBLE } from "${params.modules}${params.fs}spades${params.fs}assemble${params.fs}main"
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21 include { DUMP_SOFTWARE_VERSIONS } from "${params.modules}${params.fs}custom${params.fs}dump_software_versions${params.fs}main"
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22
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23
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24
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25 /*
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26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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27 INPUTS AND ANY CHECKS FOR THE CENTRIFLAKEN-HY WORKFLOW
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28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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29 */
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30
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31 def spades_custom_hmm = (params.spades_hmm ? file ( "${params.spades_hmm}" ) : false)
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32 def reads_platform = 0
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33
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34 reads_platform += (params.input ? 1 : 0)
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35
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36 if (spades_custom_hmm && !spades_custom_hmm.exists()) {
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37 stopNow("Please check if the following SPAdes' custom HMM directory\n" +
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38 "path is valid:\n${params.spades_hmm}\nCannot proceed further!")
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39 }
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40
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41 if (reads_platform < 1 || reads_platform == 0) {
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42 stopNow("Please mention at least one absolute path to input folder which contains\n" +
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43 "FASTQ files sequenced using the --input option.\n" +
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44 "Ex: --input (Illumina or Generic short reads in FASTQ format)")
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45 }
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46
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47 /*
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48 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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49 RUN THE CENTRIFLAKEN-HY WORKFLOW
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50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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51 */
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52
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53 workflow SPADES_ONLY {
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54 main:
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55 ch_dummy = Channel.fromPath("${params.dummyfile}")
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56 ch_dummy2 = Channel.fromPath("${params.dummyfile2}")
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57
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58 log.info summaryOfParams()
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59
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60 PROCESS_FASTQ()
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61 .processed_reads
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62 .set { ch_processed_reads }
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63
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64 PROCESS_FASTQ
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65 .out
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66 .versions
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67 .set { software_versions }
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68
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69 // As of 06/02/2022, with the upcoming newer versions of NextFlow, we will be able to do
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70 // allowNull: true for both input and output, but until then, we have to use dummy files.
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71 // and work arounds.
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72 // https://github.com/nextflow-io/nextflow/pull/2893
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73
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74 SPADES_ASSEMBLE (
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75 ch_processed_reads
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76 .combine(ch_dummy)
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77 .combine(ch_dummy2)
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78 )
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79
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80 SPADES_ASSEMBLE
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81 .out
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82 .assembly
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83 .set { ch_assembly }
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84
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85 software_versions
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86 .mix ( SPADES_ASSEMBLE.out.versions.ifEmpty(null) )
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87 .set { software_versions }
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88
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89
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90 DUMP_SOFTWARE_VERSIONS (
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91 software_versions
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92 .unique()
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93 .collectFile(name: 'collected_versions.yml')
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94 )
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95 }
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96
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97 /*
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98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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99 ON COMPLETE, SHOW GORY DETAILS OF ALL PARAMS WHICH WILL BE HELPFUL TO DEBUG
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100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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101 */
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102
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103 workflow.onComplete {
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104 if (workflow.success) {
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105 sendMail()
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106 }
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107 }
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108
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109 workflow.onError {
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110 sendMail()
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111 }
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112
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113 /*
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114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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115 HELPER METHODS FOR CENTRIFLAKEN-HY WORKFLOW
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116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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117 */
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118
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119 def help() {
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120
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121 Map helptext = [:]
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122
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123 helptext.putAll (
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124 fastqEntryPointHelp() +
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125 spadesHelp(params).text +
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126 wrapUpHelp()
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127 )
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128
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129 return addPadding(helptext)
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130 } |
