Fix nf-core#1212

drpatelh · Jul 20, 2021 · fc3ed65 · fc3ed65
1 parent c7bd944
commit fc3ed65
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Showing 3 changed files with 17 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Template
 
 * Update Nextflow installation link in pipeline template ([#1201](https://github.com/nf-core/tools/issues/1201))
+* Command `hostname` is not portable [[#1212](https://github.com/nf-core/tools/pull/1212)]
 
 ### General
 

diff --git a/nf_core/pipeline-template/lib/NfcoreTemplate.groovy b/nf_core/pipeline-template/lib/NfcoreTemplate.groovy
@@ -24,17 +24,21 @@ class NfcoreTemplate {
     public static void hostName(workflow, params, log) {
         Map colors = logColours(params.monochrome_logs)
         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)) {
-                        log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
-                            "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
-                            "      but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
-                            "      ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
-                            "=${colors.yellow}====================================================${colors.reset}="
+            try {
+                def hostname = "hostname".execute().text.trim()
+                params.hostnames.each { prof, hnames ->
+                    hnames.each { hname ->
+                        if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
+                            log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
+                                "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
+                                "      but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
+                                "      ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
+                                "=${colors.yellow}====================================================${colors.reset}="
+                        }
                     }
                 }
+            } catch (all) {
+                log.warn "[$workflow.manifest.name] Could not determine 'hostname'. Skipping check."
             }
         }
     }

diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf
@@ -130,7 +130,9 @@ workflow {{ short_name|upper }} {
 */
 
 workflow.onComplete {
-    NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+    if (params.email || params.email_on_fail) {
+        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
+    }
     NfcoreTemplate.summary(workflow, params, log)
 }