From f1a99a8d17d0cee3240824884a3fbfe96db9b616 Mon Sep 17 00:00:00 2001
From: Florian De Temmerman <florian.detemmerman@pixelgen.com>
Date: Wed, 11 Oct 2023 16:10:38 +0200
Subject: [PATCH] support remote outdir paths in email function
---
CHANGELOG.md | 2 +-
.../lib/NfcoreTemplate.groovy | 21 +++++++++++--------
2 files changed, 13 insertions(+), 10 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index a903531429..95237594ed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@
### Template
-- Support remote paths when dumping pipeline parameters into a json file ([#2465](https://github.com/nf-core/tools/pull/2465)
+- Fix writing files to a remote outdir in the NfcoreTemplate helper functions ([#2465](https://github.com/nf-core/tools/pull/2465)
### Linting
diff --git a/nf_core/pipeline-template/lib/NfcoreTemplate.groovy b/nf_core/pipeline-template/lib/NfcoreTemplate.groovy
index d2686b60ac..0f8d021a03 100755
--- a/nf_core/pipeline-template/lib/NfcoreTemplate.groovy
+++ b/nf_core/pipeline-template/lib/NfcoreTemplate.groovy
@@ -142,12 +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 $email_address (sendmail)-"
} catch (all) {
// Catch failures and try with plaintext
def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
- if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
+ if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
mail_cmd += [ '-A', mqc_report ]
}
mail_cmd.execute() << email_html
@@ -156,14 +158,16 @@ class NfcoreTemplate {
}
// Write summary e-mail HTML to a file
- def output_d = new File("${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()
}
//
@@ -234,8 +238,7 @@ class NfcoreTemplate {
def jsonStr = JsonOutput.toJson(params)
temp_pf.text = JsonOutput.prettyPrint(jsonStr)
- def destination = "${params.outdir}/pipeline_info/params_${timestamp}.json"
- FilesEx.copyTo(temp_pf.toPath(), destination)
+ FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
temp_pf.delete()
}