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NfcoreTemplate.groovy
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NfcoreTemplate.groovy
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//
// This file holds several functions used within the nf-core pipeline template.
//
import org.yaml.snakeyaml.Yaml
class NfcoreTemplate {
//
// Check AWS Batch related parameters have been specified correctly
//
public static void awsBatch(workflow, params) {
if (workflow.profile.contains('awsbatch')) {
// Check params.awsqueue and params.awsregion have been set if running on AWSBatch
assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
// Check outdir paths to be S3 buckets if running on AWSBatch
assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
}
}
//
// Warn if a -profile or Nextflow config has not been provided to run the pipeline
//
public static void checkConfigProvided(workflow, log) {
if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
"This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
" (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" +
" (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" +
" (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" +
"Please refer to the quick start section and usage docs for the pipeline.\n "
}
}
//
// Construct and send completion email
//
public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {
// Set up the e-mail variables
def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
if (!workflow.success) {
subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
}
def summary = [:]
for (group in summary_params.keySet()) {
summary << summary_params[group]
}
def misc_fields = [:]
misc_fields['Date Started'] = workflow.start
misc_fields['Date Completed'] = workflow.complete
misc_fields['Pipeline script file path'] = workflow.scriptFile
misc_fields['Pipeline script hash ID'] = workflow.scriptId
if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository
if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId
if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision
misc_fields['Nextflow Version'] = workflow.nextflow.version
misc_fields['Nextflow Build'] = workflow.nextflow.build
misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
def email_fields = [:]
email_fields['version'] = workflow.manifest.version
email_fields['runName'] = workflow.runName
email_fields['success'] = workflow.success
email_fields['dateComplete'] = workflow.complete
email_fields['duration'] = workflow.duration
email_fields['exitStatus'] = workflow.exitStatus
email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
email_fields['errorReport'] = (workflow.errorReport ?: 'None')
email_fields['commandLine'] = workflow.commandLine
email_fields['projectDir'] = workflow.projectDir
email_fields['summary'] = summary << misc_fields
// On success try attach the multiqc report
def mqc_report = null
try {
if (workflow.success) {
mqc_report = multiqc_report.getVal()
if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
if (mqc_report.size() > 1) {
log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
}
mqc_report = mqc_report[0]
}
}
} catch (all) {
if (multiqc_report) {
log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
}
}
// Check if we are only sending emails on failure
def email_address = params.email
if (!params.email && params.email_on_fail && !workflow.success) {
email_address = params.email_on_fail
}
// Render the TXT template
def engine = new groovy.text.GStringTemplateEngine()
def tf = new File("$projectDir/assets/email_template.txt")
def txt_template = engine.createTemplate(tf).make(email_fields)
def email_txt = txt_template.toString()
// Render the HTML template
def hf = new File("$projectDir/assets/email_template.html")
def html_template = engine.createTemplate(hf).make(email_fields)
def email_html = html_template.toString()
// Render the sendmail template
def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit
def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
def sf = new File("$projectDir/assets/sendmail_template.txt")
def sendmail_template = engine.createTemplate(sf).make(smail_fields)
def sendmail_html = sendmail_template.toString()
// Send the HTML e-mail
Map colors = logColours(params.monochrome_logs)
if (email_address) {
try {
if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
// Try to send HTML e-mail using sendmail
[ 'sendmail', '-t' ].execute() << sendmail_html
log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
} catch (all) {
// Catch failures and try with plaintext
def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
mail_cmd += [ '-A', mqc_report ]
}
mail_cmd.execute() << email_html
log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
}
}
// Write summary e-mail HTML to a file
def output_d = new File("${params.outdir}/pipeline_info/")
if (!output_d.exists()) {
output_d.mkdirs()
}
def output_hf = new File(output_d, "pipeline_report.html")
output_hf.withWriter { w -> w << email_html }
def output_tf = new File(output_d, "pipeline_report.txt")
output_tf.withWriter { w -> w << email_txt }
}
//
// Construct and send adaptive card
// https://adaptivecards.io
//
public static void adaptivecard(workflow, params, summary_params, projectDir, log) {
def hook_url = params.hook_url
def summary = [:]
for (group in summary_params.keySet()) {
summary << summary_params[group]
}
def misc_fields = [:]
misc_fields['start'] = workflow.start
misc_fields['complete'] = workflow.complete
misc_fields['scriptfile'] = workflow.scriptFile
misc_fields['scriptid'] = workflow.scriptId
if (workflow.repository) misc_fields['repository'] = workflow.repository
if (workflow.commitId) misc_fields['commitid'] = workflow.commitId
if (workflow.revision) misc_fields['revision'] = workflow.revision
misc_fields['nxf_version'] = workflow.nextflow.version
misc_fields['nxf_build'] = workflow.nextflow.build
misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp
def msg_fields = [:]
msg_fields['version'] = workflow.manifest.version
msg_fields['runName'] = workflow.runName
msg_fields['success'] = workflow.success
msg_fields['dateComplete'] = workflow.complete
msg_fields['duration'] = workflow.duration
msg_fields['exitStatus'] = workflow.exitStatus
msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
msg_fields['errorReport'] = (workflow.errorReport ?: 'None')
msg_fields['commandLine'] = workflow.commandLine
msg_fields['projectDir'] = workflow.projectDir
msg_fields['summary'] = summary << misc_fields
// Render the JSON template
def engine = new groovy.text.GStringTemplateEngine()
def hf = new File("$projectDir/assets/adaptivecard.json")
def json_template = engine.createTemplate(hf).make(msg_fields)
def json_message = json_template.toString()
// POST
def post = new URL(hook_url).openConnection();
post.setRequestMethod("POST")
post.setDoOutput(true)
post.setRequestProperty("Content-Type", "application/json")
post.getOutputStream().write(json_message.getBytes("UTF-8"));
def postRC = post.getResponseCode();
if (! postRC.equals(200)) {
log.warn(post.getErrorStream().getText());
}
}
//
// Print pipeline summary on completion
//
public static void summary(workflow, params, log) {
Map colors = logColours(params.monochrome_logs)
if (workflow.success) {
if (workflow.stats.ignoredCount == 0) {
log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
} else {
log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
}
} else {
log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
}
}
//
// ANSII Colours used for terminal logging
//
public static Map logColours(Boolean monochrome_logs) {
Map colorcodes = [:]
// Reset / Meta
colorcodes['reset'] = monochrome_logs ? '' : "\033[0m"
colorcodes['bold'] = monochrome_logs ? '' : "\033[1m"
colorcodes['dim'] = monochrome_logs ? '' : "\033[2m"
colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
colorcodes['blink'] = monochrome_logs ? '' : "\033[5m"
colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m"
colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m"
// Regular Colors
colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m"
colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m"
colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m"
colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m"
colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m"
colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m"
colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m"
colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m"
// Bold
colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m"
colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m"
colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m"
colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m"
colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m"
colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m"
colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m"
colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m"
// Underline
colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m"
colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m"
colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m"
colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m"
colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m"
colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m"
colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m"
colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m"
// High Intensity
colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m"
colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m"
colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m"
colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m"
colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m"
colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m"
colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m"
colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m"
// Bold High Intensity
colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m"
colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m"
colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m"
colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m"
colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m"
colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m"
colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m"
colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m"
return colorcodes
}
//
// Does what is says on the tin
//
public static String dashedLine(monochrome_logs) {
Map colors = logColours(monochrome_logs)
return "-${colors.dim}----------------------------------------------------${colors.reset}-"
}
//
// nf-core logo
//
public static String logo(workflow, monochrome_logs) {
Map colors = logColours(monochrome_logs)
String.format(
"""\n
${dashedLine(monochrome_logs)}{% if branded %}
${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset}
${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset}
${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset}
${colors.green}`._,._,\'${colors.reset}{% endif %}
${colors.purple} ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
${dashedLine(monochrome_logs)}
""".stripIndent()
)
}
}