--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.7.0/lib/routines.nf	Mon Jul 15 10:42:02 2024 -0400
@@ -0,0 +1,391 @@
+// Hold methods to print:
+//      1. Colored logo.
+//      2. Summary of parameters.
+//      3. Single dashed line.
+//      4. Double dashed line.
+//
+
+import groovy.json.JsonSlurper
+import nextflow.config.ConfigParser
+// import groovy.json.JsonOutput
+
+// ASCII logo
+def pipelineBanner() {
+
+    def padding = (params.pad) ?: 30
+    Map fgcolors = getANSIColors()
+
+    def banner = [
+        name: "${fgcolors.magenta}${workflow.manifest.name}${fgcolors.reset}",
+        author: "${fgcolors.cyan}${workflow.manifest.author}${fgcolors.reset}",
+        // workflow: "${fgcolors.magenta}${params.pipeline}${fgcolors.reset}",
+        version:  "${fgcolors.green}${workflow.manifest.version}${fgcolors.reset}",
+        center: "${fgcolors.green}${params.center}${fgcolors.reset}",
+        pad: padding
+    ]
+
+    manifest = addPadding(banner)
+
+    return """${fgcolors.white}${dashedLine(type: '=')}${fgcolors.magenta}
+             (o)                  
+  ___  _ __   _  _ __    ___  ___ 
+ / __|| '_ \\ | || '_ \\  / _ \\/ __|
+| (__ | |_) || || |_) ||  __/\\__ \\
+ \\___|| .__/ |_|| .__/  \\___||___/
+      | |       | |               
+      |_|       |_|${fgcolors.reset}
+${dashedLine()}
+${fgcolors.blue}A collection of modular pipelines at CFSAN, FDA.${fgcolors.reset}
+${dashedLine()}
+${manifest}
+${dashedLine(type: '=')}
+""".stripIndent()
+}
+
+// Add padding to keys so that
+// they indent nicely on the
+// terminal
+def addPadding(values) {
+
+    def pad = (params.pad) ?: 30
+    values.pad = pad
+
+    def padding = values.pad.toInteger()
+    def nocapitalize = values.nocapitalize
+    def stopnow = values.stopNow
+    def help = values.help
+
+    values.removeAll { 
+        k, v -> [
+            'nocapitalize',
+            'pad',
+            'stopNow',
+            'help'
+        ].contains(k)
+    }
+
+    values.keySet().each { k ->
+        v = values[k]
+        s = params.linewidth - (pad + 5)
+        if (v.toString().size() > s && !stopnow) {
+            def sen = ''
+            // v.toString().findAll(/.{1,${s}}\b(?:\W*|\s*)/).each {
+            //     sen += ' '.multiply(padding + 2) + it + '\n'
+            // }
+            v.toString().eachMatch(/.{1,${s}}(?=.*)\b|\w+/) {
+                sen += ' '.multiply(padding + 2) + it.trim() + '\n'
+            }
+            values[k] = (
+                help ? sen.replaceAll(/^(\n|\s)*/, '') : sen.trim()
+            )
+        } else {
+            values[k] = (help ? v + "\n" : v)
+        }
+        k = k.replaceAll(/\./, '_')
+    }
+
+    return values.findResults {
+        k, v -> nocapitalize ?
+            k.padRight(padding) + ': ' + v :
+            k.capitalize().padRight(padding) + ': ' + v
+    }.join("\n")
+}
+
+// Method for error messages
+def stopNow(msg) {
+
+    Map fgcolors = getANSIColors()
+    Map errors = [:]
+
+    if (msg == null) {
+        msg = "Unknown error"
+    }
+
+    errors['stopNow'] = true
+    errors["${params.cfsanpipename} - ${params.pipeline} - ERROR"] = """
+${fgcolors.reset}${dashedLine()}
+${fgcolors.red}${msg}${fgcolors.reset}
+${dashedLine()}
+""".stripIndent()
+    // println dashedLine() // defaults to stdout
+    // log.info addPadding(errors) // prints to stdout
+    exit 1, "\n" + dashedLine() +
+        "${fgcolors.red}\n" + addPadding(errors)
+}
+
+// Method to validate 4 required parameters
+// if input for entry point is FASTQ files
+def validateParamsForFASTQ() {
+    switch (params) {
+        case { params.metadata == null && params.input == null }:
+            stopNow("Either metadata CSV file with 5 required columns\n" +
+                "in order: sample, fq1, fq2, strandedness, single_end or \n" +
+                "input directory of only FASTQ files (gzipped or unzipped) should be provided\n" +
+                "using --metadata or --input options.\n" +
+                "None of these two options were provided!")
+            break
+        case { params.metadata != null && params.input != null }:
+            stopNow("Either metadata or input directory of FASTQ files\n" +
+                "should be provided using --metadata or --input options.\n" +
+                "Using both these options is not allowed!")
+            break
+        case { params.output == null }:
+            stopNow("Please mention output directory to store all results " +
+                "using --output option!")
+            break
+    }
+    return 1
+}
+
+// Method to print summary of parameters 
+// before running
+def summaryOfParams() {
+
+    def pipeline_specific_config = new ConfigParser().setIgnoreIncludes(true).parse(
+        file("${params.workflowsconf}${params.fs}${params.pipeline}.config").text
+    )
+    Map fgcolors = getANSIColors()
+    Map globalparams = [:]
+    Map localparams = params.subMap(
+        pipeline_specific_config.params.keySet().toList() + params.logtheseparams
+    )
+
+    if (localparams !instanceof Map) {
+        stopNow("Need a Map of paramters. We got: " + localparams.getClass())
+    }
+
+    if (localparams.size() != 0) {
+        localparams['nocapitalize'] = true
+        globalparams['nocapitalize'] = true
+        globalparams['nextflow_version'] = "${nextflow.version}"
+        globalparams['nextflow_build'] = "${nextflow.build}"
+        globalparams['nextflow_timestamp'] = "${nextflow.timestamp}"
+        globalparams['workflow_projectDir'] = "${workflow.projectDir}"
+        globalparams['workflow_launchDir'] = "${workflow.launchDir}"
+        globalparams['workflow_workDir'] = "${workflow.workDir}"
+        globalparams['workflow_container'] = "${workflow.container}"
+        globalparams['workflow_containerEngine'] = "${workflow.containerEngine}"
+        globalparams['workflow_runName'] = "${workflow.runName}"
+        globalparams['workflow_sessionId'] = "${workflow.sessionId}"
+        globalparams['workflow_profile'] = "${workflow.profile}"
+        globalparams['workflow_start'] = "${workflow.start}"
+        globalparams['workflow_commandLine'] = "${workflow.commandLine}"
+        return """${dashedLine()}
+Summary of the current workflow (${fgcolors.magenta}${params.pipeline}${fgcolors.reset}) parameters
+${dashedLine()}
+${addPadding(localparams)}
+${dashedLine()}
+${fgcolors.cyan}N E X T F L O W${fgcolors.reset} - ${fgcolors.magenta}${params.cfsanpipename}${fgcolors.reset} - Runtime metadata
+${dashedLine()}
+${addPadding(globalparams)}
+${dashedLine()}""".stripIndent()
+    }
+    return 1
+}
+
+// Method to display
+// Return dashed line either '-'
+// type or '=' type
+def dashedLine(Map defaults = [:]) {
+
+    Map fgcolors = getANSIColors()
+    def line = [color: 'white', type: '-']
+
+    if (!defaults.isEmpty()) {
+        line.putAll(defaults)
+    }
+
+    return fgcolors."${line.color}" + 
+        "${line.type}".multiply(params.linewidth) +
+        fgcolors.reset
+}
+
+// Return slurped keys parsed from JSON
+def slurpJson(file) {
+    def slurped = null
+    def jsonInst = new JsonSlurper()
+
+    try {
+        slurped = jsonInst.parse(new File ("${file}"))
+    }
+    catch (Exception e) {
+        log.error 'Please check your JSON schema. Invalid JSON file: ' + file
+    }
+
+    // Declare globals for the nanofactory
+    // workflow.
+    return [keys: slurped.keySet().toList(), cparams: slurped]
+}
+
+// Default help text in a map if the entry point
+// to a pipeline is FASTQ files.
+def fastqEntryPointHelp() {
+
+    Map helptext = [:]
+    Map fgcolors = getANSIColors()
+
+    helptext['Workflow'] =  "${fgcolors.magenta}${params.pipeline}${fgcolors.reset}"
+    helptext['Author'] =  "${fgcolors.cyan}${params.workflow_built_by}${fgcolors.reset}"
+    helptext['Version'] = "${fgcolors.green}${params.workflow_version}${fgcolors.reset}\n"
+    helptext['Usage'] = "cpipes --pipeline ${params.pipeline} [options]\n"
+    helptext['Required'] = ""
+    helptext['--input'] = "Absolute path to directory containing FASTQ files. " +
+        "The directory should contain only FASTQ files as all the " +
+        "files within the mentioned directory will be read. " +
+        "Ex: --input /path/to/fastq_pass"
+    helptext['--output'] = "Absolute path to directory where all the pipeline " +
+        "outputs should be stored. Ex: --output /path/to/output"
+    helptext['Other options'] = ""
+    helptext['--metadata'] = "Absolute path to metadata CSV file containing five " +
+        "mandatory columns: sample,fq1,fq2,strandedness,single_end. The fq1 and fq2 " +
+        "columns contain absolute paths to the FASTQ files. This option can be used in place " +
+        "of --input option. This is rare. Ex: --metadata samplesheet.csv"
+    helptext['--fq_suffix'] = "The suffix of FASTQ files (Unpaired reads or R1 reads or Long reads) if " +
+        "an input directory is mentioned via --input option. Default: ${params.fq_suffix}"
+    helptext['--fq2_suffix'] = "The suffix of FASTQ files (Paired-end reads or R2 reads) if an input directory is mentioned via " +
+        "--input option. Default: ${params.fq2_suffix}"
+    helptext['--fq_filter_by_len'] = "Remove FASTQ reads that are less than this many bases. " +
+        "Default: ${params.fq_filter_by_len}"
+    helptext['--fq_strandedness'] = "The strandedness of the sequencing run. This is mostly needed " +
+        "if your sequencing run is RNA-SEQ. For most of the other runs, it is probably safe to use " +
+        "unstranded for the option. Default: ${params.fq_strandedness}"
+    helptext['--fq_single_end'] = "SINGLE-END information will be auto-detected but this option forces " +
+        "PAIRED-END FASTQ files to be treated as SINGLE-END so only read 1 information is included in " +
+        "auto-generated samplesheet. Default: ${params.fq_single_end}"
+    helptext['--fq_filename_delim'] = "Delimiter by which the file name is split to obtain sample name. " +
+        "Default: ${params.fq_filename_delim}"
+    helptext['--fq_filename_delim_idx'] = "After splitting FASTQ file name by using the --fq_filename_delim option," +
+        " all elements before this index (1-based) will be joined to create final sample name." + 
+        " Default: ${params.fq_filename_delim_idx}"
+
+    return helptext
+}
+
+// Show concise help text if configured within the main workflow.
+def conciseHelp(def tool = null) {
+    Map fgcolors = getANSIColors()
+
+    tool ?= "fastp"
+    tools = tool?.tokenize(',')
+
+    return """
+${dashedLine()}
+Show configurable CLI options for each tool within ${fgcolors.magenta}${params.pipeline}${fgcolors.reset}
+${dashedLine()}
+Ex: cpipes --pipeline ${params.pipeline} --help
+""" + (tools.size() > 1 ? "Ex: cpipes --pipeline ${params.pipeline} --help ${tools[0]}"
+    + """
+Ex: cpipes --pipeline ${params.pipeline} --help ${tools[0]},${tools[1]}
+${dashedLine()}""".stripIndent() : """Ex: cpipes --pipeline ${params.pipeline} --help ${tool}
+${dashedLine()}""".stripIndent())
+
+}
+
+// Wrap help text with the following options
+def wrapUpHelp() {
+
+    return [
+        'Help options' : "",
+        '--help': "Display this message.\n",
+        'help': true,
+        'nocapitalize': true
+    ]
+}
+
+// Method to send email on workflow complete.
+def sendMail() {
+
+    if (params.user_email == null) {
+        return 1
+    }
+
+    def pad = (params.pad) ?: 30
+    def contact_emails = [
+        stakeholder: (params.workflow_blueprint_by ?: 'Not defined'),
+        author: (params.workflow_built_by ?: 'Not defined')
+    ]
+    def msg = """
+${pipelineBanner()}
+${summaryOfParams()}
+${params.cfsanpipename} - ${params.pipeline}
+${dashedLine()}
+Please check the following directory for N E X T F L O W
+reports. You can view the HTML files directly by double clicking
+them on your workstation.
+${dashedLine()}
+${params.tracereportsdir}
+${dashedLine()}
+Please send any bug reports to CFSAN Dev Team or the author or
+the stakeholder of the current pipeline.
+${dashedLine()}
+Error messages (if any)
+${dashedLine()}
+${workflow.errorMessage}
+${workflow.errorReport}
+${dashedLine()}
+Contact emails
+${dashedLine()}
+${addPadding(contact_emails)}
+${dashedLine()}
+Thank you for using ${params.cfsanpipename} - ${params.pipeline}!
+${dashedLine()}
+""".stripIndent()
+
+    def mail_cmd = [
+        'sendmail',
+        '-f', 'noreply@gmail.com',
+        '-F', 'noreply',
+        '-t', "${params.user_email}"
+    ]
+
+    def email_subject = "${params.cfsanpipename} - ${params.pipeline}"
+    Map fgcolors = getANSIColors()
+
+    if (workflow.success) {
+        email_subject += ' completed successfully!'
+    }
+    else if (!workflow.success) {
+        email_subject += ' has failed!'
+    }
+
+    try {
+        ['env', 'bash'].execute() << """${mail_cmd.join(' ')}
+Subject: ${email_subject}
+Mime-Version: 1.0
+Content-Type: text/html
+<pre>
+${msg.replaceAll(/\x1b\[[0-9;]*m/, '')}
+</pre>
+""".stripIndent()
+    } catch (all) {
+        def warning_msg = "${fgcolors.yellow}${params.cfsanpipename} - ${params.pipeline} - WARNING"
+            .padRight(pad) + ':'
+        log.info """
+${dashedLine()}
+${warning_msg}
+${dashedLine()}
+Could not send mail with the sendmail command!
+${dashedLine()}
+""".stripIndent()
+    }
+    return 1
+}
+
+// Set ANSI colors for any and all
+// STDOUT or STDERR
+def getANSIColors() {
+
+    Map fgcolors = [:]
+
+    fgcolors['reset']   = "\033[0m"
+    fgcolors['black']   = "\033[0;30m"
+    fgcolors['red']     = "\033[0;31m"
+    fgcolors['green']   = "\033[0;32m"
+    fgcolors['yellow']  = "\033[0;33m"
+    fgcolors['blue']    = "\033[0;34m"
+    fgcolors['magenta'] = "\033[0;35m"
+    fgcolors['cyan']    = "\033[0;36m"
+    fgcolors['white']   = "\033[0;37m"
+
+    return fgcolors
+}