#!/usr/bin/env nextflow
/*
========================================================================================
nf-core/hic
========================================================================================
nf-core/hic Analysis Pipeline.
#### Homepage / Documentation
https://github.com/nf-core/hic
----------------------------------------------------------------------------------------
*/
def helpMessage() {
// TODO nf-core: Add to this help message with new command line parameters
log.info"""
=======================================================
,--./,-.
___ __ __ __ ___ /,-._.--~\'
|\\ | |__ __ / ` / \\ |__) |__ } {
| \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,
`._,._,\'
nf-core/hic v${workflow.manifest.version}
=======================================================
Usage:
The typical command for running the pipeline is as follows:
nextflow run nf-core/hic --reads '*_R{1,2}.fastq.gz' -profile docker
Mandatory arguments:
--reads Path to input data (must be surrounded with quotes)
--genome Name of iGenomes reference
-profile Configuration profile to use. Can use multiple (comma separated)
Available: conda, docker, singularity, awsbatch, test and more.
Options:
--singleEnd Specifies that the input is single end reads
References If not specified in the configuration file or you wish to overwrite any of the references.
--fasta Path to Fasta reference
Other options:
--outdir The output directory where the results will be saved
--email Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits
-name Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic.
AWSBatch options:
--awsqueue The AWSBatch JobQueue that needs to be set when running on AWSBatch
--awsregion The AWS Region for your AWS Batch job to run on
""".stripIndent()
}
/*
* SET UP CONFIGURATION VARIABLES
*/
// Show help emssage
if (params.help){
helpMessage()
exit 0
}
// TODO nf-core: Add any reference files that are needed
// Configurable reference genomes
fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
if ( params.fasta ){
fasta = file(params.fasta)
if( !fasta.exists() ) exit 1, "Fasta file not found: ${params.fasta}"
}
//
// NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
// If you want to use the above in a process, define the following:
// input:
// file fasta from fasta
//
// Has the run name been specified by the user?
// this has the bonus effect of catching both -name and --name
custom_runName = params.name
if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){
custom_runName = workflow.runName
}
if( workflow.profile == 'awsbatch') {
// AWSBatch sanity checking
if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
if (!workflow.workDir.startsWith('s3') || !params.outdir.startsWith('s3')) exit 1, "Specify S3 URLs for workDir and outdir parameters on AWSBatch!"
// Check workDir/outdir paths to be S3 buckets if running on AWSBatch
// related: https://github.com/nextflow-io/nextflow/issues/813
if (!workflow.workDir.startsWith('s3:') || !params.outdir.startsWith('s3:')) exit 1, "Workdir or Outdir not on S3 - specify S3 Buckets for each to run on AWSBatch!"
}
// Stage config files
ch_multiqc_config = Channel.fromPath(params.multiqc_config)
ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
/*
* Create a channel for input read files
*/
if(params.readPaths){
if(params.singleEnd){
Channel
.from(params.readPaths)
.map { row -> [ row[0], [file(row[1][0])]] }
.ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
.into { read_files_fastqc; read_files_trimming }
} else {
Channel
.from(params.readPaths)
.map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
.ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
.into { read_files_fastqc; read_files_trimming }
}
} else {
Channel
.fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
.ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --singleEnd on the command line." }
.into { read_files_fastqc; read_files_trimming }
}
// Header log info
log.info """=======================================================
,--./,-.
___ __ __ __ ___ /,-._.--~\'
|\\ | |__ __ / ` / \\ |__) |__ } {
| \\| | \\__, \\__/ | \\ |___ \\`-._,-`-,
`._,._,\'
nf-core/hic v${workflow.manifest.version}"
======================================================="""
def summary = [:]
summary['Pipeline Name'] = 'nf-core/hic'
summary['Pipeline Version'] = workflow.manifest.version
summary['Run Name'] = custom_runName ?: workflow.runName
// TODO nf-core: Report custom parameters here
summary['Reads'] = params.reads
summary['Fasta Ref'] = params.fasta
summary['Data Type'] = params.singleEnd ? 'Single-End' : 'Paired-End'
summary['Max Memory'] = params.max_memory
summary['Max CPUs'] = params.max_cpus
summary['Max Time'] = params.max_time
summary['Output dir'] = params.outdir
summary['Working dir'] = workflow.workDir
summary['Container Engine'] = workflow.containerEngine
if(workflow.containerEngine) summary['Container'] = workflow.container
summary['Current home'] = "$HOME"
summary['Current user'] = "$USER"
summary['Current path'] = "$PWD"
summary['Working dir'] = workflow.workDir
summary['Output dir'] = params.outdir
summary['Script dir'] = workflow.projectDir
summary['Config Profile'] = workflow.profile
if(workflow.profile == 'awsbatch'){
summary['AWS Region'] = params.awsregion
summary['AWS Queue'] = params.awsqueue
}
if(params.email) summary['E-mail Address'] = params.email
log.info summary.collect { k,v -> "${k.padRight(15)}: $v" }.join("\n")
log.info "========================================="
def create_workflow_summary(summary) {
def yaml_file = workDir.resolve('workflow_summary_mqc.yaml')
yaml_file.text = """
id: 'nf-core-hic-summary'
description: " - this information is collected when the pipeline is started."
section_name: 'nf-core/hic Workflow Summary'
section_href: 'https://github.com/nf-core/hic'
plot_type: 'html'
data: |
<dl class=\"dl-horizontal\">
${summary.collect { k,v -> " <dt>$k</dt><dd><samp>${v ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>" }.join("\n")}
</dl>
""".stripIndent()
return yaml_file
}
/*
* Parse software version numbers
*/
process get_software_versions {
output:
file 'software_versions_mqc.yaml' into software_versions_yaml
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"
publishDir "${params.outdir}/fastqc", mode: 'copy',
saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
input:
set val(name), file(reads) from read_files_fastqc
output:
file "*_fastqc.{zip,html}" into fastqc_results
script:
"""
fastqc -q $reads
"""
}
/*
* STEP 2 - MultiQC
*/
process multiqc {
publishDir "${params.outdir}/MultiQC", mode: 'copy'
input:
file multiqc_config from ch_multiqc_config
// TODO nf-core: Add in log files from your new processes for MultiQC to find!
file ('fastqc/*') from fastqc_results.collect().ifEmpty([])
file ('software_versions/*') from software_versions_yaml
file workflow_summary from create_workflow_summary(summary)
output:
file "*multiqc_report.html" into multiqc_report
file "*_data"
script:
rtitle = custom_runName ? "--title \"$custom_runName\"" : ''
rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : ''
// TODO nf-core: Specify which MultiQC modules to use with -m for a faster run time
"""
multiqc -f $rtitle $rfilename --config $multiqc_config .
"""
}
/*
* STEP 3 - Output Description HTML
*/
process output_documentation {
publishDir "${params.outdir}/Documentation", mode: 'copy'
input:
file output_docs from ch_output_docs
output:
file "results_description.html"
script:
"""
markdown_to_html.r $output_docs results_description.html
"""
}
/*
* Completion e-mail notification
*/
workflow.onComplete {
// Set up the e-mail variables
def subject = "[nf-core/hic] Successful: $workflow.runName"
if(!workflow.success){
subject = "[nf-core/hic] FAILED: $workflow.runName"
}
def email_fields = [:]
email_fields['version'] = workflow.manifest.version
email_fields['runName'] = custom_runName ?: workflow.runName
email_fields['success'] = workflow.success
email_fields['dateComplete'] = workflow.complete
email_fields['duration'] = workflow.duration
email_fields['exitStatus'] = workflow.exitStatus
email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
email_fields['errorReport'] = (workflow.errorReport ?: 'None')
email_fields['commandLine'] = workflow.commandLine
email_fields['projectDir'] = workflow.projectDir
email_fields['summary'] = summary
email_fields['summary']['Date Started'] = workflow.start
email_fields['summary']['Date Completed'] = workflow.complete
email_fields['summary']['Pipeline script file path'] = workflow.scriptFile
email_fields['summary']['Pipeline script hash ID'] = workflow.scriptId
if(workflow.repository) email_fields['summary']['Pipeline repository Git URL'] = workflow.repository
if(workflow.commitId) email_fields['summary']['Pipeline repository Git Commit'] = workflow.commitId
if(workflow.revision) email_fields['summary']['Pipeline Git branch/tag'] = workflow.revision
email_fields['summary']['Nextflow Version'] = workflow.nextflow.version
email_fields['summary']['Nextflow Build'] = workflow.nextflow.build
email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
// Render the TXT template
def engine = new groovy.text.GStringTemplateEngine()
def tf = new File("$baseDir/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("$baseDir/assets/email_template.html")
def html_template = engine.createTemplate(hf).make(email_fields)
def email_html = html_template.toString()
// Render the sendmail template
def smail_fields = [ email: params.email, subject: subject, email_txt: email_txt, email_html: email_html, baseDir: "$baseDir" ]
def sf = new File("$baseDir/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 (params.email) {
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/hic] Sent summary e-mail to $params.email (sendmail)"
} catch (all) {
// Catch failures and try with plaintext
[ 'mail', '-s', subject, params.email ].execute() << email_txt
log.info "[nf-core/hic] Sent summary e-mail to $params.email (mail)"
}
}
// Write summary e-mail HTML to a file
def output_d = new File( "${params.outdir}/Documentation/" )
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 }
log.info "[nf-core/hic] Pipeline Complete"
}