kkonganti@101: //
kkonganti@101: // Start nanofactory workflow. Since this is a special
kkonganti@101: // case workflow wherein most of the bioinformatics
kkonganti@101: // tools are not used, there won't be any modules or
kkonganti@101: // subworkflows and therefore all the processes 
kkonganti@101: // reside here.
kkonganti@101: //
kkonganti@101: 
kkonganti@101: // Include any necessary methods.
kkonganti@101: include { addPadding; summaryOfParams; stopNow} \
kkonganti@101:     from "${params.routines}"
kkonganti@101: 
kkonganti@101: /*
kkonganti@101: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101:     PROCESS DEFINITIONS FOR NANOFACTORY
kkonganti@101: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101: */
kkonganti@101: 
kkonganti@101: process SETPUBLISHDIR {
kkonganti@101:     label 'process_femto'
kkonganti@101:     module (params.enable_module ? params.enable_module : null)
kkonganti@101:     conda  (params.enable_conda ? params.enable_conda : null)
kkonganti@101: 
kkonganti@101:     input:
kkonganti@101:         val options
kkonganti@101: 
kkonganti@101:     output:
kkonganti@101:         stdout
kkonganti@101: 
kkonganti@101:     shell:
kkonganti@101:         '''
kkonganti@101:         project_setup.py -s !{options.sample_sheet} \
kkonganti@101:             !{options.alt_settings} !{options.verbose} -b
kkonganti@101:         '''
kkonganti@101: }
kkonganti@101: 
kkonganti@101: process PROJECTSETUP {
kkonganti@101:     label 'process_femto'
kkonganti@101:     publishDir "${publish_dir.trim()}", mode: 'copy', overwrite: false
kkonganti@101:     module (params.enable_module ? params.enable_module : null)
kkonganti@101:     conda  (params.enable_conda ? params.enable_conda : null)
kkonganti@101: 
kkonganti@101:     input:
kkonganti@101:         val options
kkonganti@101:         val publish_dir
kkonganti@101:     
kkonganti@101:     output:
kkonganti@101:         stdout
kkonganti@101: 
kkonganti@101:     script:
kkonganti@101:         params.publish_dir = "${publish_dir.trim()}"
kkonganti@101: 
kkonganti@101:     shell:
kkonganti@101:         '''
kkonganti@101:         project_setup.py -y -s !{options.sample_sheet} !{options.alt_settings} \
kkonganti@101:             !{options.purge} !{options.runtype} !{options.logfile} \
kkonganti@101:             !{options.loglevel} !{options.verbose} !{options.nocopy} \
kkonganti@101:             !{options.fix_existing}
kkonganti@101: 
kkonganti@101:         cat < original_source.txt
kkonganti@101:         '''
kkonganti@101: }
kkonganti@101: 
kkonganti@101: process TRIMDEMUX {
kkonganti@101:     label 'process_pico'
kkonganti@101:     module (params.enable_module ? params.enable_module : null)
kkonganti@101:     conda  (params.enable_conda ? params.enable_conda : null)
kkonganti@101:     cpus "${params.guppy_threads}"
kkonganti@101: 
kkonganti@101:     input:
kkonganti@101:         val options
kkonganti@101:         val original_source
kkonganti@101: 
kkonganti@101:     output:
kkonganti@101:         path 'source.txt'
kkonganti@101: 
kkonganti@101:     shell:
kkonganti@101:         '''
kkonganti@101:         trim_demux.py -s !{options.sample_sheet} !{options.verbose} \
kkonganti@101:             !{options.alt_settings} !{options.guppy_config} -t !{options.guppy_threads}
kkonganti@101:         '''
kkonganti@101: }
kkonganti@101: 
kkonganti@101: /*
kkonganti@101: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101:     WORKFLOW ENTRY POINT
kkonganti@101: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101: */
kkonganti@101: 
kkonganti@101: workflow NANOFACTORY {
kkonganti@101: 
kkonganti@101:     if ( params.help ) {
kkonganti@101:         log.info help()
kkonganti@101:     } else if ( params.sample_sheet == null ||
kkonganti@101:         params.sample_sheet.length() == 0 ) {
kkonganti@101:         
kkonganti@101:         log.info help()
kkonganti@101:         stopNow("Please provide absolute path to a JSON formatted sample sheet using the\n" + 
kkonganti@101:             "--sample_sheet option.")
kkonganti@101:     } else {
kkonganti@101:         log.info summaryOfParams()
kkonganti@101: 
kkonganti@101:         options = Channel.empty()
kkonganti@101:         Channel
kkonganti@101:             .from(setOptions())
kkonganti@101:             .set { options }
kkonganti@101: 
kkonganti@101:         take:
kkonganti@101:             options
kkonganti@101: 
kkonganti@101:         main:
kkonganti@101:             SETPUBLISHDIR(options)
kkonganti@101:             PROJECTSETUP(options, SETPUBLISHDIR.out)
kkonganti@101:             TRIMDEMUX(options, PROJECTSETUP.out)
kkonganti@101:     }
kkonganti@101: }
kkonganti@101: 
kkonganti@101: 
kkonganti@101: /*
kkonganti@101: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101:     THE END
kkonganti@101: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101: */
kkonganti@101: 
kkonganti@101: 
kkonganti@101: /*
kkonganti@101: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101:     HELPER METHODS FOR NANOFACTORY WORKFLOW
kkonganti@101: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
kkonganti@101: */
kkonganti@101: 
kkonganti@101: def setOptions() {
kkonganti@101: 
kkonganti@101:     Map options = [:]
kkonganti@101: 
kkonganti@101:     options['sample_sheet'] ?= "${params.sample_sheet}"
kkonganti@101:     options['verbose'] = params.verbose ? "-v" : ""
kkonganti@101:     options['alt_settings'] = params.global_settings ? "-c ${params.global_settings}" : ""
kkonganti@101:     options['purge'] = params.setup_purge_existing ? "-p" : ""
kkonganti@101:     options['logfile'] = params.log_file ? "-l ${params.log_file}" : ""
kkonganti@101:     options['loglevel'] = params.log_level ? "--loglevel ${params.log_level}" : ""
kkonganti@101:     options['nocopy'] = params.setup_nocopy ? "--nocopy" : ""
kkonganti@101:     options['runtype'] = params.setup_runtype ? "-r ${params.setup_runtype}" : ""
kkonganti@101:     options['fix_existing'] = params.setup_fix_existing ? "-f" : ""
kkonganti@101:     options['guppy_config'] = params.guppy_config ? " -g ${params.guppy_config}" : ""
kkonganti@101:     options['mode'] = params.mode ? "-m ${params.mode}" : "-m prod"
kkonganti@101:     options['mail_group'] = params.mail_group ? "-g ${params.mail_group}" : "-g stakeholders"
kkonganti@101:     options['guppy_threads'] = params.guppy_threads ? "${params.guppy_threads}" : 1
kkonganti@101:     options['pad'] = pad.toInteger()
kkonganti@101:     options['nocapitalize'] = true
kkonganti@101:     
kkonganti@101:     return options
kkonganti@101: }
kkonganti@101: 
kkonganti@101: def help() {
kkonganti@101: 
kkonganti@101:     Map helptext = [:]
kkonganti@101: 
kkonganti@101:     helptext['help'] = true
kkonganti@101:     helptext['nocapitalize'] = true
kkonganti@101:     helptext['Workflow'] =  "${params.pipeline}"
kkonganti@101:     helptext['Author'] = "${params.workflow_author}"
kkonganti@101:     helptext['Version'] = "${params.workflow_version}\n"
kkonganti@101:     helptext['Usage'] = "cpipes --pipeline nanofactory [options]\n"
kkonganti@101:     helptext['Required'] = ""
kkonganti@101:     helptext['--sample_sheet'] = "The JSON-formatted sample sheet for this run. Normally provided by Pore Refiner.\n"
kkonganti@101:     helptext['Other options'] = ""
kkonganti@101:     helptext['--global_settings'] = "An alternate global settings file.  If not present the installed default will be used."
kkonganti@101:     helptext['--log_file'] = "Path and file name to a log file relative to the project directory (Default: 'logs/workflow.log')"
kkonganti@101:     helptext['--log_level'] = "One of 'debug', 'info', 'warning', 'error', 'fatal' (Default: 'info')"
kkonganti@101:     helptext['--mode'] = "Set the run mode.  One of 'dev', 'test', 'stage', or 'prod' (Default: 'prod')"
kkonganti@101:     helptext['--verbose'] = "Use to enable more verbose console output from each tool\n"
kkonganti@101:     helptext['Project setup options'] = ""
kkonganti@101:     helptext['--disable_project_setup'] = "Do not do project setup (Default:  setup is enabled)"
kkonganti@101:     helptext['--setup_purge_existing'] = "Before setting up the project area delete any existing files (Default: don't purge)"
kkonganti@101:     helptext['--setup_nocopy'] = "During setup, do NOT copy the original data files to the scrach location (Default: copy)"
kkonganti@101:     helptext['--setup_runtype'] = "Set things up for the indicated run type (Currently not used)"
kkonganti@101:     helptext['--setup_runtype'] = "Set things up for the indicated run type (Currently not used)"
kkonganti@101:     helptext['--enable_module'] = "Software environment module. Ex: --enable_module 'nanofactory/current'"
kkonganti@101:     helptext['--enable_conda'] = "CONDA environment module. Ex: --enable_conda nanofactory\n"
kkonganti@101:     helptext['Help options'] = ""
kkonganti@101:     helptext['--help'] = "Display this message.\n"
kkonganti@101: 
kkonganti@101:     return addPadding(helptext)
kkonganti@101: }