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new File --> file #354

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Jul 3, 2019
Merged

new File --> file #354

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f247e5b
new File --> file
olgabot Jul 3, 2019
da7fb8d
Use `file()` instead of `new File`
olgabot Jul 3, 2019
0bd384d
Add comment in changelog
olgabot Jul 3, 2019
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,9 @@
* Add proper `nf-core` logo for tools
* Add `Quick Start` section to main README of template
* Fix [Docker RunOptions](https://github.com/nf-core/tools/pull/351) to get UID and GID set in the template
* Use [`file`](https://github.com/nf-core/tools/pull/354) instead of `new File`
to avoid weird behavior such as making an `s3:/` directory locally when using
an AWS S3 bucket as the `--outdir`.

#### Other

Expand Down
58 changes: 29 additions & 29 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/main.nf
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Expand Up @@ -49,7 +49,7 @@ def helpMessage() {
* SET UP CONFIGURATION VARIABLES
*/

// Show help message
// Show help emssage
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Suggested change
// Show help emssage
// Show help message

if (params.help){
helpMessage()
exit 0
Expand All @@ -65,7 +65,7 @@ if (params.genomes && params.genome && !params.genomes.containsKey(params.genome
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}"
if( !fasta.exists() ) exit 1, "Fasta file not found: ${params.fasta}"
}
//
// NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY
Expand All @@ -78,12 +78,12 @@ if ( params.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]+/) ){
if( !(workflow.runName ==~ /[a-z]+_[a-z]+/) ){
custom_runName = workflow.runName
}


if ( workflow.profile == 'awsbatch') {
if( workflow.profile == '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
Expand All @@ -100,8 +100,8 @@ ch_output_docs = Channel.fromPath("$baseDir/docs/output.md")
/*
* Create a channel for input read files
*/
if (params.readPaths){
if (params.singleEnd){
if(params.readPaths){
if(params.singleEnd){
Channel
.from(params.readPaths)
.map { row -> [ row[0], [file(row[1][0])]] }
Expand All @@ -125,28 +125,28 @@ if (params.readPaths){
// Header log info
log.info nfcoreHeader()
def summary = [:]
if (workflow.revision) summary['Pipeline Release'] = workflow.revision
if(workflow.revision) summary['Pipeline Release'] = workflow.revision
summary['Run Name'] = custom_runName ?: workflow.runName
// TODO nf-core: Report custom parameters here
summary['Reads'] = params.reads
summary['Fasta Ref'] = params.fasta
summary['Data Type'] = params.singleEnd ? 'Single-End' : 'Paired-End'
summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
if(workflow.containerEngine) summary['Container'] = "$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 == 'awsbatch'){
if(workflow.profile == 'awsbatch'){
summary['AWS Region'] = params.awsregion
summary['AWS Queue'] = params.awsqueue
}
summary['Config Profile'] = workflow.profile
if (params.config_profile_description) summary['Config Description'] = params.config_profile_description
if (params.config_profile_contact) summary['Config Contact'] = params.config_profile_contact
if (params.config_profile_url) summary['Config URL'] = params.config_profile_url
if (params.email) {
if(params.config_profile_description) summary['Config Description'] = params.config_profile_description
if(params.config_profile_contact) summary['Config Contact'] = params.config_profile_contact
if(params.config_profile_url) summary['Config URL'] = params.config_profile_url
if(params.email) {
summary['E-mail Address'] = params.email
summary['MultiQC maxsize'] = params.maxMultiqcEmailFileSize
}
Expand Down Expand Up @@ -279,7 +279,7 @@ workflow.onComplete {

// Set up the e-mail variables
def subject = "[{{ cookiecutter.name }}] Successful: $workflow.runName"
if (!workflow.success){
if(!workflow.success){
subject = "[{{ cookiecutter.name }}] FAILED: $workflow.runName"
}
def email_fields = [:]
Expand All @@ -298,10 +298,10 @@ workflow.onComplete {
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
if (workflow.container) email_fields['summary']['Docker image'] = workflow.container
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
if(workflow.container) email_fields['summary']['Docker image'] = workflow.container
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
Expand Down Expand Up @@ -341,7 +341,7 @@ workflow.onComplete {
// Send the HTML e-mail
if (params.email) {
try {
if ( params.plaintext_email ){ throw GroovyException('Send plaintext e-mail, not HTML') }
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 "[{{ cookiecutter.name }}] Sent summary e-mail to $params.email (sendmail)"
Expand All @@ -353,27 +353,27 @@ workflow.onComplete {
}

// Write summary e-mail HTML to a file
def output_d = new File( "${params.outdir}/pipeline_info/" )
if ( !output_d.exists() ) {
def output_d = file( "${params.outdir}/pipeline_info/" )
if( !output_d.exists() ) {
output_d.mkdirs()
}
def output_hf = new File( output_d, "pipeline_report.html" )
def output_hf = file( output_d, "pipeline_report.html" )
output_hf.withWriter { w -> w << email_html }
def output_tf = new File( output_d, "pipeline_report.txt" )
def output_tf = file( output_d, "pipeline_report.txt" )
output_tf.withWriter { w -> w << email_txt }

c_reset = params.monochrome_logs ? '' : "\033[0m";
c_purple = params.monochrome_logs ? '' : "\033[0;35m";
c_green = params.monochrome_logs ? '' : "\033[0;32m";
c_red = params.monochrome_logs ? '' : "\033[0;31m";

if (workflow.stats.ignoredCount > 0 && workflow.success) {
if (workflow.stats.ignoredCountFmt > 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} ${c_reset}"
log.info "${c_red}Number of ignored errored process(es) : ${workflow.stats.ignoredCountFmt} ${c_reset}"
log.info "${c_green}Number of successfully ran process(es) : ${workflow.stats.succeedCountFmt} ${c_reset}"
}

if (workflow.success){
if(workflow.success){
log.info "${c_purple}[{{ cookiecutter.name }}]${c_green} Pipeline completed successfully${c_reset}"
} else {
checkHostname()
Expand Down Expand Up @@ -411,11 +411,11 @@ def checkHostname(){
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){
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)){
if(hostname.contains(hname) && !workflow.profile.contains(prof)){
log.error "====================================================\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" +
Expand Down