copy NfcoreTemplate.groovy from nf-core template 2.11dev

nf-core · Nov 10, 2023 · 34be89e · 34be89e
1 parent 4ca08ac
commit 34be89e
Showing 1 changed file with 14 additions and 9 deletions.
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
@@ -4,6 +4,7 @@
 
 import org.yaml.snakeyaml.Yaml
 import groovy.json.JsonOutput
+import nextflow.extension.FilesEx
 
 class NfcoreTemplate {
 
@@ -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
@@ -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()
     }
 
     //
@@ -337,12 +342,12 @@ class NfcoreTemplate {
         String workflow_version = NfcoreTemplate.version(workflow)
         String.format(
             """\n
-            ${dashedLine(monochrome_logs)}
+            ${dashedLine(monochrome_logs)}{% if branded %}
                                                     ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
             ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
             ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
             ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
-                                                    ${colors.green}`._,._,\'${colors.reset}
+                                                    ${colors.green}`._,._,\'${colors.reset}{% endif %}
             ${colors.purple}  ${workflow.manifest.name} ${workflow_version}${colors.reset}
             ${dashedLine(monochrome_logs)}
             """.stripIndent()