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1 //
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2 // Start nanofactory workflow. Since this is a special
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3 // case workflow wherein most of the bioinformatics
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4 // tools are not used, there won't be any modules or
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5 // subworkflows and therefore all the processes
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6 // reside here.
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7 //
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8
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9 // Include any necessary methods.
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10 include { addPadding; summaryOfParams; stopNow} \
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11 from "${params.routines}"
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12
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13 /*
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14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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15 PROCESS DEFINITIONS FOR NANOFACTORY
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16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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17 */
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18
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19 process SETPUBLISHDIR {
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20 label 'process_femto'
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21 module (params.enable_module ? params.enable_module : null)
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22 conda (params.enable_conda ? params.enable_conda : null)
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23
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24 input:
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25 val options
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26
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27 output:
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28 stdout
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29
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30 shell:
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31 '''
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32 project_setup.py -s !{options.sample_sheet} \
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33 !{options.alt_settings} !{options.verbose} -b
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34 '''
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35 }
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36
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37 process PROJECTSETUP {
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38 label 'process_femto'
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39 publishDir "${publish_dir.trim()}", mode: 'copy', overwrite: false
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40 module (params.enable_module ? params.enable_module : null)
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41 conda (params.enable_conda ? params.enable_conda : null)
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42
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43 input:
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44 val options
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45 val publish_dir
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46
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47 output:
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48 stdout
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49
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50 script:
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51 params.publish_dir = "${publish_dir.trim()}"
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52
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53 shell:
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54 '''
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55 project_setup.py -y -s !{options.sample_sheet} !{options.alt_settings} \
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56 !{options.purge} !{options.runtype} !{options.logfile} \
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57 !{options.loglevel} !{options.verbose} !{options.nocopy} \
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58 !{options.fix_existing}
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59
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60 cat < original_source.txt
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61 '''
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62 }
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63
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64 process TRIMDEMUX {
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65 label 'process_pico'
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66 module (params.enable_module ? params.enable_module : null)
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67 conda (params.enable_conda ? params.enable_conda : null)
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68 cpus "${params.guppy_threads}"
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69
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70 input:
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71 val options
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72 val original_source
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73
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74 output:
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75 path 'source.txt'
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76
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77 shell:
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78 '''
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79 trim_demux.py -s !{options.sample_sheet} !{options.verbose} \
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80 !{options.alt_settings} !{options.guppy_config} -t !{options.guppy_threads}
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81 '''
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82 }
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83
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84 /*
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85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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86 WORKFLOW ENTRY POINT
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87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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88 */
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89
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90 workflow NANOFACTORY {
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91
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92 if ( params.help ) {
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93 log.info help()
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94 } else if ( params.sample_sheet == null ||
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95 params.sample_sheet.length() == 0 ) {
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96
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97 log.info help()
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98 stopNow("Please provide absolute path to a JSON formatted sample sheet using the\n" +
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99 "--sample_sheet option.")
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100 } else {
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101 log.info summaryOfParams()
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102
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103 options = Channel.empty()
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104 Channel
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105 .from(setOptions())
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106 .set { options }
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107
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108 take:
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109 options
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110
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111 main:
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112 SETPUBLISHDIR(options)
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113 PROJECTSETUP(options, SETPUBLISHDIR.out)
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114 TRIMDEMUX(options, PROJECTSETUP.out)
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115 }
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116 }
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117
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118
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119 /*
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120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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121 THE END
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122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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123 */
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124
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125
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126 /*
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127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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128 HELPER METHODS FOR NANOFACTORY WORKFLOW
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129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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130 */
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131
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132 def setOptions() {
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133
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134 Map options = [:]
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135
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136 options['sample_sheet'] ?= "${params.sample_sheet}"
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137 options['verbose'] = params.verbose ? "-v" : ""
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138 options['alt_settings'] = params.global_settings ? "-c ${params.global_settings}" : ""
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139 options['purge'] = params.setup_purge_existing ? "-p" : ""
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140 options['logfile'] = params.log_file ? "-l ${params.log_file}" : ""
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141 options['loglevel'] = params.log_level ? "--loglevel ${params.log_level}" : ""
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142 options['nocopy'] = params.setup_nocopy ? "--nocopy" : ""
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143 options['runtype'] = params.setup_runtype ? "-r ${params.setup_runtype}" : ""
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144 options['fix_existing'] = params.setup_fix_existing ? "-f" : ""
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145 options['guppy_config'] = params.guppy_config ? " -g ${params.guppy_config}" : ""
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146 options['mode'] = params.mode ? "-m ${params.mode}" : "-m prod"
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147 options['mail_group'] = params.mail_group ? "-g ${params.mail_group}" : "-g stakeholders"
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148 options['guppy_threads'] = params.guppy_threads ? "${params.guppy_threads}" : 1
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149 options['pad'] = pad.toInteger()
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150 options['nocapitalize'] = true
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151
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152 return options
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153 }
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154
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155 def help() {
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156
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157 Map helptext = [:]
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158
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159 helptext['help'] = true
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160 helptext['nocapitalize'] = true
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161 helptext['Workflow'] = "${params.pipeline}"
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162 helptext['Author'] = "${params.workflow_author}"
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163 helptext['Version'] = "${params.workflow_version}\n"
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164 helptext['Usage'] = "cpipes --pipeline nanofactory [options]\n"
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165 helptext['Required'] = ""
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166 helptext['--sample_sheet'] = "The JSON-formatted sample sheet for this run. Normally provided by Pore Refiner.\n"
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167 helptext['Other options'] = ""
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168 helptext['--global_settings'] = "An alternate global settings file. If not present the installed default will be used."
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169 helptext['--log_file'] = "Path and file name to a log file relative to the project directory (Default: 'logs/workflow.log')"
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170 helptext['--log_level'] = "One of 'debug', 'info', 'warning', 'error', 'fatal' (Default: 'info')"
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171 helptext['--mode'] = "Set the run mode. One of 'dev', 'test', 'stage', or 'prod' (Default: 'prod')"
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172 helptext['--verbose'] = "Use to enable more verbose console output from each tool\n"
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173 helptext['Project setup options'] = ""
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174 helptext['--disable_project_setup'] = "Do not do project setup (Default: setup is enabled)"
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175 helptext['--setup_purge_existing'] = "Before setting up the project area delete any existing files (Default: don't purge)"
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176 helptext['--setup_nocopy'] = "During setup, do NOT copy the original data files to the scrach location (Default: copy)"
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177 helptext['--setup_runtype'] = "Set things up for the indicated run type (Currently not used)"
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178 helptext['--setup_runtype'] = "Set things up for the indicated run type (Currently not used)"
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179 helptext['--enable_module'] = "Software environment module. Ex: --enable_module 'nanofactory/current'"
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180 helptext['--enable_conda'] = "CONDA environment module. Ex: --enable_conda nanofactory\n"
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181 helptext['Help options'] = ""
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182 helptext['--help'] = "Display this message.\n"
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183
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184 return addPadding(helptext)
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185 }
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