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main.nf
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#!/usr/bin/env nextflow
/*
========================================================================================
nf-core/spliz
========================================================================================
nf-core/spliz Analysis Pipeline.
#### Homepage / Documentation
https://github.com/salzmanlab/SpliZ
----------------------------------------------------------------------------------------
*/
nextflow.enable.dsl=2
log.info Headers.nf_core(workflow, params.monochrome_logs)
////////////////////////////////////////////////////
/* -- PRINT HELP -- */
////////////////////////////////////////////////////+
def json_schema = "$projectDir/nextflow_schema.json"
if (params.help) {
def command = "nextflow run nf-core/spliz -c conf/test.config"
log.info NfcoreSchema.params_help(workflow, params, json_schema, command)
exit 0
}
////////////////////////////////////////////////////
/* -- VALIDATE PARAMETERS -- */
////////////////////////////////////////////////////+
if (params.validate_params) {
NfcoreSchema.validateParameters(params, json_schema, log)
}
////////////////////////////////////////////////////
/* -- Collect configuration parameters -- */
////////////////////////////////////////////////////
// Check if genome exists in the config file
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(', ')}"
}
// TODO nf-core: Add any reference files that are needed
// Configurable reference genomes
//
// NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
// If you want to use the channel below in a process, define the following:
// input:
// file fasta from ch_fasta
//
//params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
//if (params.fasta) { ch_fasta = file(params.fasta, checkIfExists: true) }
// Check AWS batch settings
if (workflow.profile.contains('awsbatch')) {
// AWSBatch sanity checking
if (!params.awsqueue || !params.awsregion) exit 1, 'Specify correct --awsqueue and --awsregion parameters on AWSBatch!'
// Check outdir paths to be S3 buckets if running on AWSBatch
// related: https://github.com/nextflow-io/nextflow/issues/813
if (!params.outdir.startsWith('s3:')) exit 1, 'Outdir not on S3 - specify S3 Bucket to run on AWSBatch!'
// Prevent trace files to be stored on S3 since S3 does not support rolling files.
if (params.tracedir.startsWith('s3:')) exit 1, 'Specify a local tracedir or run without trace! S3 cannot be used for tracefiles.'
}
// Stage config files
ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true)
ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
////////////////////////////////////////////////////
/* -- PRINT PARAMETER SUMMARY -- */
////////////////////////////////////////////////////
log.info NfcoreSchema.params_summary_log(workflow, params, json_schema)
// Header log info
def summary = [:]
if (workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Run Name'] = workflow.runName
// TODO nf-core: Report custom parameters here
//summary['Input'] = params.input
//summary['Fasta Ref'] = params.fasta
//summary['Data Type'] = params.single_end ? 'Single-End' : 'Paired-End'
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
summary['Output dir'] = params.outdir
summary['Launch dir'] = workflow.launchDir
summary['Working dir'] = workflow.workDir
summary['Script dir'] = workflow.projectDir
summary['User'] = workflow.userName
if (workflow.profile.contains('awsbatch')) {
summary['AWS Region'] = params.awsregion
summary['AWS Queue'] = params.awsqueue
summary['AWS CLI'] = params.awscli
}
summary['Config Profile'] = workflow.profile
if (params.config_profile_description) summary['Config Profile Description'] = params.config_profile_description
if (params.config_profile_contact) summary['Config Profile Contact'] = params.config_profile_contact
if (params.config_profile_url) summary['Config Profile URL'] = params.config_profile_url
summary['Config Files'] = workflow.configFiles.join(', ')
if (params.email || params.email_on_fail) {
summary['E-mail Address'] = params.email
summary['E-mail on failure'] = params.email_on_fail
summary['MultiQC maxsize'] = params.max_multiqc_email_size
}
// Check the hostnames against configured profiles
checkHostname()
Channel.from(summary.collect{ [it.key, it.value] })
.map { k,v -> "<dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }
.reduce { a, b -> return [a, b].join("\n ") }
.map { x -> """
id: 'nf-core-spliz-summary'
description: " - this information is collected when the pipeline is started."
section_name: 'nf-core/spliz Workflow Summary'
section_href: 'https://github.com/nf-core/spliz'
plot_type: 'html'
data: |
<dl class=\"dl-horizontal\">
$x
</dl>
""".stripIndent() }
.set { ch_workflow_summary }
/*
* Parse software version numbers
*/
process get_software_versions {
publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode,
saveAs: { filename ->
if (filename.indexOf('.csv') > 0) filename
else null
}
output:
file 'software_versions_mqc.yaml' into ch_software_versions_yaml
file 'software_versions.csv'
script:
// TODO nf-core: Get all tools to print their version number here
"""
echo $workflow.manifest.version > v_pipeline.txt
echo $workflow.nextflow.version > v_nextflow.txt
fastqc --version > v_fastqc.txt
multiqc --version > v_multiqc.txt
scrape_software_versions.py &> software_versions_mqc.yaml
"""
}
/*
* STEP 1 - FastQC
*/
process fastqc {
tag "$name"
label 'process_medium'
publishDir "${params.outdir}/fastqc", mode: params.publish_dir_mode,
saveAs: { filename ->
filename.indexOf('.zip') > 0 ? "zips/$filename" : "$filename"
}
input:
set val(name), file(reads) from ch_read_files_fastqc
output:
file '*_fastqc.{zip,html}' into ch_fastqc_results
script:
"""
fastqc --quiet --threads $task.cpus $reads
"""
}
/*
* STEP 2 - MultiQC
*/
process multiqc {
publishDir "${params.outdir}/MultiQC", mode: params.publish_dir_mode
input:
file (multiqc_config) from ch_multiqc_config
file (mqc_custom_config) from ch_multiqc_custom_config.collect().ifEmpty([])
// TODO nf-core: Add in log files from your new processes for MultiQC to find!
file ('fastqc/*') from ch_fastqc_results.collect().ifEmpty([])
file ('software_versions/*') from ch_software_versions_yaml.collect()
file workflow_summary from ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml")
output:
file "*multiqc_report.html" into ch_multiqc_report
file "*_data"
file "multiqc_plots"
script:
rtitle = ''
rfilename = ''
if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
rtitle = "--title \"${workflow.runName}\""
rfilename = "--filename " + workflow.runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report"
}
custom_config_file = params.multiqc_config ? "--config $mqc_custom_config" : ''
// TODO nf-core: Specify which MultiQC modules to use with -m for a faster run time
"""
multiqc -f $rtitle $rfilename $custom_config_file .
"""
}
/*
* STEP 3 - Output Description HTML
*/
process output_documentation {
publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode
input:
file output_docs from ch_output_docs
file images from ch_output_docs_images
output:
file 'results_description.html'
script:
"""
markdown_to_html.py $output_docs -o results_description.html
"""
}
/*
========================================================================================
IMPORT LOCAL MODULES/SUBWORKFLOWS
========================================================================================
*/
include { SPLIZ_PIPELINE } from './workflows/spliz_pipeline'
/*
========================================================================================
MAIN WORKFLOW
========================================================================================
*/
workflow NFCORE_SPLIZ {
SPLIZ_PIPELINE ()
}
workflow {
NFCORE_SPLIZ ()
}
/*
* Completion e-mail notification
*/
workflow.onComplete {
// Set up the e-mail variables
def subject = "[nf-core/spliz] Successful: $workflow.runName"
if (!workflow.success) {
subject = "[nf-core/spliz] FAILED: $workflow.runName"
}
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
email_fields['summary']['Date Started'] = workflow.start
email_fields['summary']['Date Completed'] = workflow.complete
email_fields['summary']['Pipeline script file path'] = workflow.scriptFile
email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId
if (workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
if (workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
if (workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
/*
// TODO nf-core: If not using MultiQC, strip out this code (including params.max_multiqc_email_size)
// On success try attach the multiqc report
def mqc_report = null
try {
if (workflow.success) {
mqc_report = ch_multiqc_report.getVal()
if (mqc_report.getClass() == ArrayList) {
log.warn "[nf-core/spliz] Found multiple reports from process 'multiqc', will use only one"
mqc_report = mqc_report[0]
}
}
} catch (all) {
log.warn "[nf-core/spliz] Could not attach MultiQC report to summary email"
}
*/
// Check if we are only sending emails on failure
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("$projectDir/assets/email_template.html")
def html_template = engine.createTemplate(hf).make(email_fields)
def email_html = html_template.toString()
// Render the sendmail template
def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: params.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
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 "[nf-core/spliz] 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() <= params.max_multiqc_email_size.toBytes() ) {
mail_cmd += [ '-A', mqc_report ]
}
mail_cmd.execute() << email_html
log.info "[nf-core/spliz] 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 }
c_green = params.monochrome_logs ? '' : "\033[0;32m";
c_purple = params.monochrome_logs ? '' : "\033[0;35m";
c_red = params.monochrome_logs ? '' : "\033[0;31m";
c_reset = params.monochrome_logs ? '' : "\033[0m";
if (workflow.stats.ignoredCount > 0 && workflow.success) {
log.info "-${c_purple}Warning, pipeline completed, but with errored process(es) ${c_reset}-"
log.info "-${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCount} ${c_reset}-"
log.info "-${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCount} ${c_reset}-"
}
if (workflow.success) {
log.info "-${c_purple}[nf-core/spliz]${c_green} Pipeline completed successfully${c_reset}-"
log.info "Results can be found in ${params.outdir}."
} else {
checkHostname()
log.info "-${c_purple}[nf-core/spliz]${c_red} Pipeline completed with errors${c_reset}-"
}
}
workflow.onError {
// Print unexpected parameters - easiest is to just rerun validation
NfcoreSchema.validateParameters(params, json_schema, log)
}
def checkHostname() {
def c_reset = params.monochrome_logs ? '' : "\033[0m"
def c_white = params.monochrome_logs ? '' : "\033[0;37m"
def c_red = params.monochrome_logs ? '' : "\033[1;91m"
def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m"
if (params.hostnames) {
def hostname = 'hostname'.execute().text.trim()
params.hostnames.each { prof, hnames ->
hnames.each { hname ->
if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
log.error "${c_red}====================================================${c_reset}\n" +
" ${c_red}WARNING!${c_reset} You are running with `-profile $workflow.profile`\n" +
" but your machine hostname is ${c_white}'$hostname'${c_reset}\n" +
" ${c_yellow_bold}It's highly recommended that you use `-profile $prof${c_reset}`\n" +
"${c_red}====================================================${c_reset}\n"
}
}
}
}
}