342 lines
16 KiB
Groovy
342 lines
16 KiB
Groovy
//
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// This file holds several functions used within the nf-core pipeline template.
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//
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// MIT License
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//
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// Copyright (c) 2018 nf-core
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//
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// Permission is hereby granted, free of charge, to any person obtaining a copy
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// of this software and associated documentation files (the "Software"), to deal
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// in the Software without restriction, including without limitation the rights
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// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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// copies of the Software, and to permit persons to whom the Software is
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// furnished to do so, subject to the following conditions:
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//
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// The above copyright notice and this permission notice shall be included in all
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// copies or substantial portions of the Software.
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//
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// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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// SOFTWARE.
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import org.yaml.snakeyaml.Yaml
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class NfcoreTemplate {
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//
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// Check AWS Batch related parameters have been specified correctly
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//
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public static void awsBatch(workflow, params) {
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if (workflow.profile.contains('awsbatch')) {
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// Check params.awsqueue and params.awsregion have been set if running on AWSBatch
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assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
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// Check outdir paths to be S3 buckets if running on AWSBatch
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assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
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}
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}
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//
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// Check params.hostnames
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//
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public static void hostName(workflow, params, log) {
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Map colors = logColours(params.monochrome_logs)
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if (params.hostnames) {
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try {
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def hostname = "hostname".execute().text.trim()
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params.hostnames.each { prof, hnames ->
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hnames.each { hname ->
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if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
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log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
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"${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
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" but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
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" ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
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"=${colors.yellow}====================================================${colors.reset}="
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}
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}
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}
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} catch (Exception e) {
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log.warn "[$workflow.manifest.name] Could not determine 'hostname' - skipping check. Reason: ${e.message}."
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}
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}
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}
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//
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// Generate version string
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//
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public static String version(workflow) {
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String version_string = ""
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if (workflow.manifest.version) {
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def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
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version_string += "${prefix_v}${workflow.manifest.version}"
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}
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if (workflow.commitId) {
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def git_shortsha = workflow.commitId.substring(0, 7)
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version_string += "-g${git_shortsha}"
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}
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return version_string
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}
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//
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// Construct and send completion email
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//
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public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[], fail_mapped_reads=[:]) {
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// Set up the e-mail variables
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def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
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if (fail_mapped_reads.size() > 0) {
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subject = "[$workflow.manifest.name] Partially successful (${fail_mapped_reads.size()} skipped): $workflow.runName"
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}
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if (!workflow.success) {
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subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
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}
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def summary = [:]
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for (group in summary_params.keySet()) {
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summary << summary_params[group]
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}
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def misc_fields = [:]
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misc_fields['Date Started'] = workflow.start
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misc_fields['Date Completed'] = workflow.complete
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misc_fields['Pipeline script file path'] = workflow.scriptFile
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misc_fields['Pipeline script hash ID'] = workflow.scriptId
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if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository
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if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId
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if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision
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misc_fields['Nextflow Version'] = workflow.nextflow.version
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misc_fields['Nextflow Build'] = workflow.nextflow.build
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misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
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def email_fields = [:]
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email_fields['version'] = NfcoreTemplate.version(workflow)
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email_fields['runName'] = workflow.runName
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email_fields['success'] = workflow.success
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email_fields['dateComplete'] = workflow.complete
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email_fields['duration'] = workflow.duration
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email_fields['exitStatus'] = workflow.exitStatus
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email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
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email_fields['errorReport'] = (workflow.errorReport ?: 'None')
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email_fields['commandLine'] = workflow.commandLine
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email_fields['projectDir'] = workflow.projectDir
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email_fields['summary'] = summary << misc_fields
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email_fields['fail_mapped_reads'] = fail_mapped_reads.keySet()
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email_fields['min_mapped_reads'] = params.min_mapped_reads
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// On success try attach the multiqc report
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def mqc_report = null
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try {
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if (workflow.success && !params.skip_multiqc) {
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mqc_report = multiqc_report.getVal()
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if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
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if (mqc_report.size() > 1) {
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log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
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}
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mqc_report = mqc_report[0]
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}
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}
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} catch (all) {
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if (multiqc_report) {
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log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
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}
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}
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// Check if we are only sending emails on failure
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def email_address = params.email
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if (!params.email && params.email_on_fail && !workflow.success) {
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email_address = params.email_on_fail
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}
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// Render the TXT template
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def engine = new groovy.text.GStringTemplateEngine()
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def tf = new File("$projectDir/assets/email_template.txt")
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def txt_template = engine.createTemplate(tf).make(email_fields)
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def email_txt = txt_template.toString()
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// Render the HTML template
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def hf = new File("$projectDir/assets/email_template.html")
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def html_template = engine.createTemplate(hf).make(email_fields)
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def email_html = html_template.toString()
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// Render the sendmail template
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def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit
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def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
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def sf = new File("$projectDir/assets/sendmail_template.txt")
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def sendmail_template = engine.createTemplate(sf).make(smail_fields)
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def sendmail_html = sendmail_template.toString()
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// Send the HTML e-mail
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Map colors = logColours(params.monochrome_logs)
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if (email_address) {
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try {
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if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
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// Try to send HTML e-mail using sendmail
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[ 'sendmail', '-t' ].execute() << sendmail_html
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log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
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} catch (all) {
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// Catch failures and try with plaintext
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def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
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if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
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mail_cmd += [ '-A', mqc_report ]
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}
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mail_cmd.execute() << email_html
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log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
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}
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}
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// Write summary e-mail HTML to a file
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def output_d = new File("${params.outdir}/pipeline_info/")
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if (!output_d.exists()) {
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output_d.mkdirs()
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}
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def output_hf = new File(output_d, "pipeline_report.html")
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output_hf.withWriter { w -> w << email_html }
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def output_tf = new File(output_d, "pipeline_report.txt")
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output_tf.withWriter { w -> w << email_txt }
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}
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//
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// Print pipeline summary on completion
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//
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public static void summary(workflow, params, log, fail_mapped_reads=[:], pass_mapped_reads=[:]) {
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Map colors = logColours(params.monochrome_logs)
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if (pass_mapped_reads.size() > 0) {
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def idx = 0
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def samp_aln = ''
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def total_aln_count = pass_mapped_reads.size() + fail_mapped_reads.size()
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for (samp in pass_mapped_reads) {
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samp_aln += " ${samp.value}: ${samp.key}\n"
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idx += 1
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if (idx > 5) {
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samp_aln += " ..see pipeline reports for full list\n"
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break;
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}
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}
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log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} ${pass_mapped_reads.size()}/$total_aln_count samples passed Bowtie2 ${params.min_mapped_reads} mapped read threshold:\n${samp_aln}${colors.reset}-"
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}
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if (fail_mapped_reads.size() > 0) {
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def samp_aln = ''
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for (samp in fail_mapped_reads) {
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samp_aln += " ${samp.value}: ${samp.key}\n"
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}
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log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} ${fail_mapped_reads.size()} samples skipped since they failed Bowtie2 ${params.min_mapped_reads} mapped read threshold:\n${samp_aln}${colors.reset}-"
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}
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if (workflow.success) {
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if (workflow.stats.ignoredCount == 0) {
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log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
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} else {
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log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
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}
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} else {
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hostName(workflow, params, log)
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log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
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}
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}
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//
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// ANSII Colours used for terminal logging
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//
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public static Map logColours(Boolean monochrome_logs) {
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Map colorcodes = [:]
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// Reset / Meta
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colorcodes['reset'] = monochrome_logs ? '' : "\033[0m"
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colorcodes['bold'] = monochrome_logs ? '' : "\033[1m"
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colorcodes['dim'] = monochrome_logs ? '' : "\033[2m"
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colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
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colorcodes['blink'] = monochrome_logs ? '' : "\033[5m"
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colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m"
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colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m"
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// Regular Colors
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colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m"
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colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m"
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colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m"
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colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
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colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m"
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colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
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colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m"
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colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m"
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// Bold
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colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m"
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colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m"
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colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m"
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colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
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colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m"
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colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
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colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m"
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colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m"
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// Underline
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colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m"
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colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m"
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colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m"
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colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
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colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m"
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colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
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colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m"
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colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m"
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// High Intensity
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colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m"
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colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m"
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colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m"
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colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
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colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m"
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colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
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colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m"
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colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m"
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// Bold High Intensity
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colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m"
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colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m"
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colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m"
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colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
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colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m"
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colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
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colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m"
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colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m"
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return colorcodes
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}
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//
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// Does what is says on the tin
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//
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public static String dashedLine(monochrome_logs) {
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Map colors = logColours(monochrome_logs)
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return "${colors.dim}--------------------------------------------------------------------------------${colors.reset}"
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}
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// epi2me-labs logo
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public static String logo(workflow, monochrome_logs) {
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Map colors = NfcoreTemplate.logColours(monochrome_logs)
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String workflow_name = workflow.manifest.name.split("/")[1]
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String workflow_version = version(workflow)
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String.format(
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"""
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${colors.igreen}|||||||||| ${colors.reset}${colors.dim}_____ ____ ___ ____ __ __ _____
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${colors.igreen}|||||||||| ${colors.reset}${colors.dim}| ____| _ \\_ _|___ \\| \\/ | ____|
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${colors.yellow}||||| ${colors.reset}${colors.dim}| _| | |_) | | __) | |\\/| | _|
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${colors.yellow}||||| ${colors.reset}${colors.dim}| |___| __/| | / __/| | | | |__
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${colors.iblue}|||||||||| ${colors.reset}${colors.dim}|_____|_| |___|_____|_| |_|_____|
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${colors.iblue}|||||||||| ${colors.reset}${colors.bold}${workflow_name} ${workflow_version}${colors.reset}
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${NfcoreTemplate.dashedLine(monochrome_logs)}
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""".stripIndent()
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)
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}
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}
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