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support remote paths in NfCoreTemplate:dump_parameters #2465

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merged 3 commits into from
Oct 16, 2023
Merged

support remote paths in NfCoreTemplate:dump_parameters #2465

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69c4238
support remote paths in NfCoreTemplate:dump_parameters
fbdtemme Oct 9, 2023
dc1f20c
update CHANGELOG.md
fbdtemme Oct 9, 2023
5ec389e
support remote outdir paths in email function
fbdtemme Oct 11, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@

### Template

- Fix writing files to a remote outdir in the NfcoreTemplate helper functions ([#2465](https://github.com/nf-core/tools/pull/2465)

### Linting

- Fix incorrectly failing linting if 'modules' was not found in meta.yml ([#2447](https://github.com/nf-core/tools/pull/2447))
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32 changes: 18 additions & 14 deletions nf_core/pipeline-template/lib/NfcoreTemplate.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@

import org.yaml.snakeyaml.Yaml
import groovy.json.JsonOutput
import nextflow.extension.FilesEx

class NfcoreTemplate {

Expand Down Expand Up @@ -141,12 +142,14 @@ class NfcoreTemplate {
try {
if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
// Try to send HTML e-mail using sendmail
def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
sendmail_tf.withWriter { w -> w << sendmail_html }
[ '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() ) {
if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
mail_cmd += [ '-A', mqc_report ]
}
mail_cmd.execute() << email_html
Expand All @@ -155,14 +158,16 @@ class NfcoreTemplate {
}

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

// Write summary e-mail TXT to a file
def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
output_tf.withWriter { w -> w << email_txt }
FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt");
output_tf.delete()
}

//
Expand Down Expand Up @@ -227,15 +232,14 @@ class NfcoreTemplate {
// Dump pipeline parameters in a json file
//
public static void dump_parameters(workflow, params) {
def output_d = new File("${params.outdir}/pipeline_info/")
if (!output_d.exists()) {
output_d.mkdirs()
}

def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
def output_pf = new File(output_d, "params_${timestamp}.json")
def filename = "params_${timestamp}.json"
def temp_pf = new File(workflow.launchDir.toString(), ".${filename}")
def jsonStr = JsonOutput.toJson(params)
output_pf.text = JsonOutput.prettyPrint(jsonStr)
temp_pf.text = JsonOutput.prettyPrint(jsonStr)

FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
temp_pf.delete()
}

//
Expand Down