kkonganti@11: // Hold methods to print:
kkonganti@11: //      1. Colored logo.
kkonganti@11: //      2. Summary of parameters.
kkonganti@11: //      3. Single dashed line.
kkonganti@11: //      4. Double dashed line.
kkonganti@11: //
kkonganti@11: 
kkonganti@11: import groovy.json.JsonSlurper
kkonganti@11: import nextflow.config.ConfigParser
kkonganti@11: // import groovy.json.JsonOutput
kkonganti@11: 
kkonganti@11: // ASCII logo
kkonganti@11: def pipelineBanner() {
kkonganti@11: 
kkonganti@11:     def padding = (params.pad) ?: 30
kkonganti@11:     Map fgcolors = getANSIColors()
kkonganti@11: 
kkonganti@11:     def banner = [
kkonganti@11:         name: "${fgcolors.magenta}${workflow.manifest.name}${fgcolors.reset}",
kkonganti@11:         author: "${fgcolors.cyan}${workflow.manifest.author}${fgcolors.reset}",
kkonganti@11:         // workflow: "${fgcolors.magenta}${params.pipeline}${fgcolors.reset}",
kkonganti@11:         version:  "${fgcolors.green}${workflow.manifest.version}${fgcolors.reset}",
kkonganti@11:         center: "${fgcolors.green}${params.center}${fgcolors.reset}",
kkonganti@11:         pad: padding
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     manifest = addPadding(banner)
kkonganti@11: 
kkonganti@11:     return """${fgcolors.white}${dashedLine(type: '=')}${fgcolors.magenta}
kkonganti@11:              (o)                  
kkonganti@11:   ___  _ __   _  _ __    ___  ___ 
kkonganti@11:  / __|| '_ \\ | || '_ \\  / _ \\/ __|
kkonganti@11: | (__ | |_) || || |_) ||  __/\\__ \\
kkonganti@11:  \\___|| .__/ |_|| .__/  \\___||___/
kkonganti@11:       | |       | |               
kkonganti@11:       |_|       |_|${fgcolors.reset}
kkonganti@11: ${dashedLine()}
kkonganti@11: ${fgcolors.blue}A collection of modular pipelines at CFSAN, FDA.${fgcolors.reset}
kkonganti@11: ${dashedLine()}
kkonganti@11: ${manifest}
kkonganti@11: ${dashedLine(type: '=')}
kkonganti@11: """.stripIndent()
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Add padding to keys so that
kkonganti@11: // they indent nicely on the
kkonganti@11: // terminal
kkonganti@11: def addPadding(values) {
kkonganti@11: 
kkonganti@11:     def pad = (params.pad) ?: 30
kkonganti@11:     values.pad = pad
kkonganti@11: 
kkonganti@11:     def padding = values.pad.toInteger()
kkonganti@11:     def nocapitalize = values.nocapitalize
kkonganti@11:     def stopnow = values.stopNow
kkonganti@11:     def help = values.help
kkonganti@11: 
kkonganti@11:     values.removeAll { 
kkonganti@11:         k, v -> [
kkonganti@11:             'nocapitalize',
kkonganti@11:             'pad',
kkonganti@11:             'stopNow',
kkonganti@11:             'help'
kkonganti@11:         ].contains(k)
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     values.keySet().each { k ->
kkonganti@11:         v = values[k]
kkonganti@11:         s = params.linewidth - (pad + 5)
kkonganti@11:         if (v.toString().size() > s && !stopnow) {
kkonganti@11:             def sen = ''
kkonganti@11:             // v.toString().findAll(/.{1,${s}}\b(?:\W*|\s*)/).each {
kkonganti@11:             //     sen += ' '.multiply(padding + 2) + it + '\n'
kkonganti@11:             // }
kkonganti@11:             v.toString().eachMatch(/.{1,${s}}(?=.*)\b|\w+/) {
kkonganti@11:                 sen += ' '.multiply(padding + 2) + it.trim() + '\n'
kkonganti@11:             }
kkonganti@11:             values[k] = (
kkonganti@11:                 help ? sen.replaceAll(/^(\n|\s)*/, '') : sen.trim()
kkonganti@11:             )
kkonganti@11:         } else {
kkonganti@11:             values[k] = (help ? v + "\n" : v)
kkonganti@11:         }
kkonganti@11:         k = k.replaceAll(/\./, '_')
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return values.findResults {
kkonganti@11:         k, v -> nocapitalize ?
kkonganti@11:             k.padRight(padding) + ': ' + v :
kkonganti@11:             k.capitalize().padRight(padding) + ': ' + v
kkonganti@11:     }.join("\n")
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Method for error messages
kkonganti@11: def stopNow(msg) {
kkonganti@11: 
kkonganti@11:     Map fgcolors = getANSIColors()
kkonganti@11:     Map errors = [:]
kkonganti@11: 
kkonganti@11:     if (msg == null) {
kkonganti@11:         msg = "Unknown error"
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     errors['stopNow'] = true
kkonganti@11:     errors["${params.cfsanpipename} - ${params.pipeline} - ERROR"] = """
kkonganti@11: ${fgcolors.reset}${dashedLine()}
kkonganti@11: ${fgcolors.red}${msg}${fgcolors.reset}
kkonganti@11: ${dashedLine()}
kkonganti@11: """.stripIndent()
kkonganti@11:     // println dashedLine() // defaults to stdout
kkonganti@11:     // log.info addPadding(errors) // prints to stdout
kkonganti@11:     exit 1, "\n" + dashedLine() +
kkonganti@11:         "${fgcolors.red}\n" + addPadding(errors)
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Method to validate 4 required parameters
kkonganti@11: // if input for entry point is FASTQ files
kkonganti@11: def validateParamsForFASTQ() {
kkonganti@11:     switch (params) {
kkonganti@11:         case { params.metadata == null && params.input == null }:
kkonganti@11:             stopNow("Either metadata CSV file with 5 required columns\n" +
kkonganti@11:                 "in order: sample, fq1, fq2, strandedness, single_end or \n" +
kkonganti@11:                 "input directory of only FASTQ files (gzipped or unzipped) should be provided\n" +
kkonganti@11:                 "using --metadata or --input options.\n" +
kkonganti@11:                 "None of these two options were provided!")
kkonganti@11:             break
kkonganti@11:         case { params.metadata != null && params.input != null }:
kkonganti@11:             stopNow("Either metadata or input directory of FASTQ files\n" +
kkonganti@11:                 "should be provided using --metadata or --input options.\n" +
kkonganti@11:                 "Using both these options is not allowed!")
kkonganti@11:             break
kkonganti@11:         case { params.output == null }:
kkonganti@11:             stopNow("Please mention output directory to store all results " +
kkonganti@11:                 "using --output option!")
kkonganti@11:             break
kkonganti@11:     }
kkonganti@11:     return 1
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Method to print summary of parameters 
kkonganti@11: // before running
kkonganti@11: def summaryOfParams() {
kkonganti@11: 
kkonganti@11:     def pipeline_specific_config = new ConfigParser().setIgnoreIncludes(true).parse(
kkonganti@11:         file("${params.workflowsconf}${params.fs}${params.pipeline}.config").text
kkonganti@11:     )
kkonganti@11:     Map fgcolors = getANSIColors()
kkonganti@11:     Map globalparams = [:]
kkonganti@11:     Map localparams = params.subMap(
kkonganti@11:         pipeline_specific_config.params.keySet().toList() + params.logtheseparams
kkonganti@11:     )
kkonganti@11: 
kkonganti@11:     if (localparams !instanceof Map) {
kkonganti@11:         stopNow("Need a Map of paramters. We got: " + localparams.getClass())
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     if (localparams.size() != 0) {
kkonganti@11:         localparams['nocapitalize'] = true
kkonganti@11:         globalparams['nocapitalize'] = true
kkonganti@11:         globalparams['nextflow_version'] = "${nextflow.version}"
kkonganti@11:         globalparams['nextflow_build'] = "${nextflow.build}"
kkonganti@11:         globalparams['nextflow_timestamp'] = "${nextflow.timestamp}"
kkonganti@11:         globalparams['workflow_projectDir'] = "${workflow.projectDir}"
kkonganti@11:         globalparams['workflow_launchDir'] = "${workflow.launchDir}"
kkonganti@11:         globalparams['workflow_workDir'] = "${workflow.workDir}"
kkonganti@11:         globalparams['workflow_container'] = "${workflow.container}"
kkonganti@11:         globalparams['workflow_containerEngine'] = "${workflow.containerEngine}"
kkonganti@11:         globalparams['workflow_runName'] = "${workflow.runName}"
kkonganti@11:         globalparams['workflow_sessionId'] = "${workflow.sessionId}"
kkonganti@11:         globalparams['workflow_profile'] = "${workflow.profile}"
kkonganti@11:         globalparams['workflow_start'] = "${workflow.start}"
kkonganti@11:         globalparams['workflow_commandLine'] = "${workflow.commandLine}"
kkonganti@11:         return """${dashedLine()}
kkonganti@11: Summary of the current workflow (${fgcolors.magenta}${params.pipeline}${fgcolors.reset}) parameters
kkonganti@11: ${dashedLine()}
kkonganti@11: ${addPadding(localparams)}
kkonganti@11: ${dashedLine()}
kkonganti@11: ${fgcolors.cyan}N E X T F L O W${fgcolors.reset} - ${fgcolors.magenta}${params.cfsanpipename}${fgcolors.reset} - Runtime metadata
kkonganti@11: ${dashedLine()}
kkonganti@11: ${addPadding(globalparams)}
kkonganti@11: ${dashedLine()}""".stripIndent()
kkonganti@11:     }
kkonganti@11:     return 1
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Method to display
kkonganti@11: // Return dashed line either '-'
kkonganti@11: // type or '=' type
kkonganti@11: def dashedLine(Map defaults = [:]) {
kkonganti@11: 
kkonganti@11:     Map fgcolors = getANSIColors()
kkonganti@11:     def line = [color: 'white', type: '-']
kkonganti@11: 
kkonganti@11:     if (!defaults.isEmpty()) {
kkonganti@11:         line.putAll(defaults)
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     return fgcolors."${line.color}" + 
kkonganti@11:         "${line.type}".multiply(params.linewidth) +
kkonganti@11:         fgcolors.reset
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Return slurped keys parsed from JSON
kkonganti@11: def slurpJson(file) {
kkonganti@11:     def slurped = null
kkonganti@11:     def jsonInst = new JsonSlurper()
kkonganti@11: 
kkonganti@11:     try {
kkonganti@11:         slurped = jsonInst.parse(new File ("${file}"))
kkonganti@11:     }
kkonganti@11:     catch (Exception e) {
kkonganti@11:         log.error 'Please check your JSON schema. Invalid JSON file: ' + file
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     // Declare globals for the nanofactory
kkonganti@11:     // workflow.
kkonganti@11:     return [keys: slurped.keySet().toList(), cparams: slurped]
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Default help text in a map if the entry point
kkonganti@11: // to a pipeline is FASTQ files.
kkonganti@11: def fastqEntryPointHelp() {
kkonganti@11: 
kkonganti@11:     Map helptext = [:]
kkonganti@11:     Map fgcolors = getANSIColors()
kkonganti@11: 
kkonganti@11:     helptext['Workflow'] =  "${fgcolors.magenta}${params.pipeline}${fgcolors.reset}"
kkonganti@11:     helptext['Author'] =  "${fgcolors.cyan}${params.workflow_built_by}${fgcolors.reset}"
kkonganti@11:     helptext['Version'] = "${fgcolors.green}${params.workflow_version}${fgcolors.reset}\n"
kkonganti@11:     helptext['Usage'] = "cpipes --pipeline ${params.pipeline} [options]\n"
kkonganti@11:     helptext['Required'] = ""
kkonganti@11:     helptext['--input'] = "Absolute path to directory containing FASTQ files. " +
kkonganti@11:         "The directory should contain only FASTQ files as all the " +
kkonganti@11:         "files within the mentioned directory will be read. " +
kkonganti@11:         "Ex: --input /path/to/fastq_pass"
kkonganti@11:     helptext['--output'] = "Absolute path to directory where all the pipeline " +
kkonganti@11:         "outputs should be stored. Ex: --output /path/to/output"
kkonganti@11:     helptext['Other options'] = ""
kkonganti@11:     helptext['--metadata'] = "Absolute path to metadata CSV file containing five " +
kkonganti@11:         "mandatory columns: sample,fq1,fq2,strandedness,single_end. The fq1 and fq2 " +
kkonganti@11:         "columns contain absolute paths to the FASTQ files. This option can be used in place " +
kkonganti@11:         "of --input option. This is rare. Ex: --metadata samplesheet.csv"
kkonganti@11:     helptext['--fq_suffix'] = "The suffix of FASTQ files (Unpaired reads or R1 reads or Long reads) if " +
kkonganti@11:         "an input directory is mentioned via --input option. Default: ${params.fq_suffix}"
kkonganti@11:     helptext['--fq2_suffix'] = "The suffix of FASTQ files (Paired-end reads or R2 reads) if an input directory is mentioned via " +
kkonganti@11:         "--input option. Default: ${params.fq2_suffix}"
kkonganti@11:     helptext['--fq_filter_by_len'] = "Remove FASTQ reads that are less than this many bases. " +
kkonganti@11:         "Default: ${params.fq_filter_by_len}"
kkonganti@11:     helptext['--fq_strandedness'] = "The strandedness of the sequencing run. This is mostly needed " +
kkonganti@11:         "if your sequencing run is RNA-SEQ. For most of the other runs, it is probably safe to use " +
kkonganti@11:         "unstranded for the option. Default: ${params.fq_strandedness}"
kkonganti@11:     helptext['--fq_single_end'] = "SINGLE-END information will be auto-detected but this option forces " +
kkonganti@11:         "PAIRED-END FASTQ files to be treated as SINGLE-END so only read 1 information is included in " +
kkonganti@11:         "auto-generated samplesheet. Default: ${params.fq_single_end}"
kkonganti@11:     helptext['--fq_filename_delim'] = "Delimiter by which the file name is split to obtain sample name. " +
kkonganti@11:         "Default: ${params.fq_filename_delim}"
kkonganti@11:     helptext['--fq_filename_delim_idx'] = "After splitting FASTQ file name by using the --fq_filename_delim option," +
kkonganti@11:         " all elements before this index (1-based) will be joined to create final sample name." + 
kkonganti@11:         " Default: ${params.fq_filename_delim_idx}"
kkonganti@11: 
kkonganti@11:     return helptext
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Show concise help text if configured within the main workflow.
kkonganti@11: def conciseHelp(def tool = null) {
kkonganti@11:     Map fgcolors = getANSIColors()
kkonganti@11: 
kkonganti@11:     tool ?= "fastp"
kkonganti@11:     tools = tool?.tokenize(',')
kkonganti@11: 
kkonganti@11:     return """
kkonganti@11: ${dashedLine()}
kkonganti@11: Show configurable CLI options for each tool within ${fgcolors.magenta}${params.pipeline}${fgcolors.reset}
kkonganti@11: ${dashedLine()}
kkonganti@11: Ex: cpipes --pipeline ${params.pipeline} --help
kkonganti@11: """ + (tools.size() > 1 ? "Ex: cpipes --pipeline ${params.pipeline} --help ${tools[0]}"
kkonganti@11:     + """
kkonganti@11: Ex: cpipes --pipeline ${params.pipeline} --help ${tools[0]},${tools[1]}
kkonganti@11: ${dashedLine()}""".stripIndent() : """Ex: cpipes --pipeline ${params.pipeline} --help ${tool}
kkonganti@11: ${dashedLine()}""".stripIndent())
kkonganti@11: 
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Wrap help text with the following options
kkonganti@11: def wrapUpHelp() {
kkonganti@11: 
kkonganti@11:     return [
kkonganti@11:         'Help options' : "",
kkonganti@11:         '--help': "Display this message.\n",
kkonganti@11:         'help': true,
kkonganti@11:         'nocapitalize': true
kkonganti@11:     ]
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Method to send email on workflow complete.
kkonganti@11: def sendMail() {
kkonganti@11: 
kkonganti@11:     if (params.user_email == null) {
kkonganti@11:         return 1
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     def pad = (params.pad) ?: 30
kkonganti@11:     def contact_emails = [
kkonganti@11:         stakeholder: (params.workflow_blueprint_by ?: 'Not defined'),
kkonganti@11:         author: (params.workflow_built_by ?: 'Not defined')
kkonganti@11:     ]
kkonganti@11:     def msg = """
kkonganti@11: ${pipelineBanner()}
kkonganti@11: ${summaryOfParams()}
kkonganti@11: ${params.cfsanpipename} - ${params.pipeline}
kkonganti@11: ${dashedLine()}
kkonganti@11: Please check the following directory for N E X T F L O W
kkonganti@11: reports. You can view the HTML files directly by double clicking
kkonganti@11: them on your workstation.
kkonganti@11: ${dashedLine()}
kkonganti@11: ${params.tracereportsdir}
kkonganti@11: ${dashedLine()}
kkonganti@11: Please send any bug reports to CFSAN Dev Team or the author or
kkonganti@11: the stakeholder of the current pipeline.
kkonganti@11: ${dashedLine()}
kkonganti@11: Error messages (if any)
kkonganti@11: ${dashedLine()}
kkonganti@11: ${workflow.errorMessage}
kkonganti@11: ${workflow.errorReport}
kkonganti@11: ${dashedLine()}
kkonganti@11: Contact emails
kkonganti@11: ${dashedLine()}
kkonganti@11: ${addPadding(contact_emails)}
kkonganti@11: ${dashedLine()}
kkonganti@11: Thank you for using ${params.cfsanpipename} - ${params.pipeline}!
kkonganti@11: ${dashedLine()}
kkonganti@11: """.stripIndent()
kkonganti@11: 
kkonganti@11:     def mail_cmd = [
kkonganti@11:         'sendmail',
kkonganti@11:         '-f', 'noreply@gmail.com',
kkonganti@11:         '-F', 'noreply',
kkonganti@11:         '-t', "${params.user_email}"
kkonganti@11:     ]
kkonganti@11: 
kkonganti@11:     def email_subject = "${params.cfsanpipename} - ${params.pipeline}"
kkonganti@11:     Map fgcolors = getANSIColors()
kkonganti@11: 
kkonganti@11:     if (workflow.success) {
kkonganti@11:         email_subject += ' completed successfully!'
kkonganti@11:     }
kkonganti@11:     else if (!workflow.success) {
kkonganti@11:         email_subject += ' has failed!'
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     try {
kkonganti@11:         ['env', 'bash'].execute() << """${mail_cmd.join(' ')}
kkonganti@11: Subject: ${email_subject}
kkonganti@11: Mime-Version: 1.0
kkonganti@11: Content-Type: text/html
kkonganti@11: <pre>
kkonganti@11: ${msg.replaceAll(/\x1b\[[0-9;]*m/, '')}
kkonganti@11: </pre>
kkonganti@11: """.stripIndent()
kkonganti@11:     } catch (all) {
kkonganti@11:         def warning_msg = "${fgcolors.yellow}${params.cfsanpipename} - ${params.pipeline} - WARNING"
kkonganti@11:             .padRight(pad) + ':'
kkonganti@11:         log.info """
kkonganti@11: ${dashedLine()}
kkonganti@11: ${warning_msg}
kkonganti@11: ${dashedLine()}
kkonganti@11: Could not send mail with the sendmail command!
kkonganti@11: ${dashedLine()}
kkonganti@11: """.stripIndent()
kkonganti@11:     }
kkonganti@11:     return 1
kkonganti@11: }
kkonganti@11: 
kkonganti@11: // Set ANSI colors for any and all
kkonganti@11: // STDOUT or STDERR
kkonganti@11: def getANSIColors() {
kkonganti@11: 
kkonganti@11:     Map fgcolors = [:]
kkonganti@11: 
kkonganti@11:     fgcolors['reset']   = "\033[0m"
kkonganti@11:     fgcolors['black']   = "\033[0;30m"
kkonganti@11:     fgcolors['red']     = "\033[0;31m"
kkonganti@11:     fgcolors['green']   = "\033[0;32m"
kkonganti@11:     fgcolors['yellow']  = "\033[0;33m"
kkonganti@11:     fgcolors['blue']    = "\033[0;34m"
kkonganti@11:     fgcolors['magenta'] = "\033[0;35m"
kkonganti@11:     fgcolors['cyan']    = "\033[0;36m"
kkonganti@11:     fgcolors['white']   = "\033[0;37m"
kkonganti@11: 
kkonganti@11:     return fgcolors
kkonganti@11: }