--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.0/workflows/nanofactory.nf	Thu Aug 04 10:45:55 2022 -0400
@@ -0,0 +1,185 @@
+//
+// Start nanofactory workflow. Since this is a special
+// case workflow wherein most of the bioinformatics
+// tools are not used, there won't be any modules or
+// subworkflows and therefore all the processes 
+// reside here.
+//
+
+// Include any necessary methods.
+include { addPadding; summaryOfParams; stopNow} \
+    from "${params.routines}"
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PROCESS DEFINITIONS FOR NANOFACTORY
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+process SETPUBLISHDIR {
+    label 'process_femto'
+    module (params.enable_module ? params.enable_module : null)
+    conda  (params.enable_conda ? params.enable_conda : null)
+
+    input:
+        val options
+
+    output:
+        stdout
+
+    shell:
+        '''
+        project_setup.py -s !{options.sample_sheet} \
+            !{options.alt_settings} !{options.verbose} -b
+        '''
+}
+
+process PROJECTSETUP {
+    label 'process_femto'
+    publishDir "${publish_dir.trim()}", mode: 'copy', overwrite: false
+    module (params.enable_module ? params.enable_module : null)
+    conda  (params.enable_conda ? params.enable_conda : null)
+
+    input:
+        val options
+        val publish_dir
+    
+    output:
+        stdout
+
+    script:
+        params.publish_dir = "${publish_dir.trim()}"
+
+    shell:
+        '''
+        project_setup.py -y -s !{options.sample_sheet} !{options.alt_settings} \
+            !{options.purge} !{options.runtype} !{options.logfile} \
+            !{options.loglevel} !{options.verbose} !{options.nocopy} \
+            !{options.fix_existing}
+
+        cat < original_source.txt
+        '''
+}
+
+process TRIMDEMUX {
+    label 'process_pico'
+    module (params.enable_module ? params.enable_module : null)
+    conda  (params.enable_conda ? params.enable_conda : null)
+    cpus "${params.guppy_threads}"
+
+    input:
+        val options
+        val original_source
+
+    output:
+        path 'source.txt'
+
+    shell:
+        '''
+        trim_demux.py -s !{options.sample_sheet} !{options.verbose} \
+            !{options.alt_settings} !{options.guppy_config} -t !{options.guppy_threads}
+        '''
+}
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    WORKFLOW ENTRY POINT
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+workflow NANOFACTORY {
+
+    if ( params.help ) {
+        log.info help()
+    } else if ( params.sample_sheet == null ||
+        params.sample_sheet.length() == 0 ) {
+        
+        log.info help()
+        stopNow("Please provide absolute path to a JSON formatted sample sheet using the\n" + 
+            "--sample_sheet option.")
+    } else {
+        log.info summaryOfParams()
+
+        options = Channel.empty()
+        Channel
+            .from(setOptions())
+            .set { options }
+
+        take:
+            options
+
+        main:
+            SETPUBLISHDIR(options)
+            PROJECTSETUP(options, SETPUBLISHDIR.out)
+            TRIMDEMUX(options, PROJECTSETUP.out)
+    }
+}
+
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    THE END
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    HELPER METHODS FOR NANOFACTORY WORKFLOW
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+def setOptions() {
+
+    Map options = [:]
+
+    options['sample_sheet'] ?= "${params.sample_sheet}"
+    options['verbose'] = params.verbose ? "-v" : ""
+    options['alt_settings'] = params.global_settings ? "-c ${params.global_settings}" : ""
+    options['purge'] = params.setup_purge_existing ? "-p" : ""
+    options['logfile'] = params.log_file ? "-l ${params.log_file}" : ""
+    options['loglevel'] = params.log_level ? "--loglevel ${params.log_level}" : ""
+    options['nocopy'] = params.setup_nocopy ? "--nocopy" : ""
+    options['runtype'] = params.setup_runtype ? "-r ${params.setup_runtype}" : ""
+    options['fix_existing'] = params.setup_fix_existing ? "-f" : ""
+    options['guppy_config'] = params.guppy_config ? " -g ${params.guppy_config}" : ""
+    options['mode'] = params.mode ? "-m ${params.mode}" : "-m prod"
+    options['mail_group'] = params.mail_group ? "-g ${params.mail_group}" : "-g stakeholders"
+    options['guppy_threads'] = params.guppy_threads ? "${params.guppy_threads}" : 1
+    options['pad'] = pad.toInteger()
+    options['nocapitalize'] = true
+    
+    return options
+}
+
+def help() {
+
+    Map helptext = [:]
+
+    helptext['help'] = true
+    helptext['nocapitalize'] = true
+    helptext['Workflow'] =  "${params.pipeline}"
+    helptext['Author'] = "${params.workflow_author}"
+    helptext['Version'] = "${params.workflow_version}\n"
+    helptext['Usage'] = "cpipes --pipeline nanofactory [options]\n"
+    helptext['Required'] = ""
+    helptext['--sample_sheet'] = "The JSON-formatted sample sheet for this run. Normally provided by Pore Refiner.\n"
+    helptext['Other options'] = ""
+    helptext['--global_settings'] = "An alternate global settings file.  If not present the installed default will be used."
+    helptext['--log_file'] = "Path and file name to a log file relative to the project directory (Default: 'logs/workflow.log')"
+    helptext['--log_level'] = "One of 'debug', 'info', 'warning', 'error', 'fatal' (Default: 'info')"
+    helptext['--mode'] = "Set the run mode.  One of 'dev', 'test', 'stage', or 'prod' (Default: 'prod')"
+    helptext['--verbose'] = "Use to enable more verbose console output from each tool\n"
+    helptext['Project setup options'] = ""
+    helptext['--disable_project_setup'] = "Do not do project setup (Default:  setup is enabled)"
+    helptext['--setup_purge_existing'] = "Before setting up the project area delete any existing files (Default: don't purge)"
+    helptext['--setup_nocopy'] = "During setup, do NOT copy the original data files to the scrach location (Default: copy)"
+    helptext['--setup_runtype'] = "Set things up for the indicated run type (Currently not used)"
+    helptext['--setup_runtype'] = "Set things up for the indicated run type (Currently not used)"
+    helptext['--enable_module'] = "Software environment module. Ex: --enable_module 'nanofactory/current'"
+    helptext['--enable_conda'] = "CONDA environment module. Ex: --enable_conda nanofactory\n"
+    helptext['Help options'] = ""
+    helptext['--help'] = "Display this message.\n"
+
+    return addPadding(helptext)
+}