adjust test resources, add in files that cant be skipped

phac-nml · Jan 2, 2025 · 5b74fee · 5b74fee
1 parent 47890aa
commit 5b74fee
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Showing 4 changed files with 103 additions and 4 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -15,8 +15,6 @@ lint:
     - assets/email_template.txt
     - assets/multiqc_config.yml
     - assets/sendmail_template.txt
-    - assets/adaptivecard.json
-    - assets/slackreport.json
     - assets/nf-core-LegioVue_logo_light.png
     - conf/igenomes.config
     - conf/igenomes_ignored.config

diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json
@@ -0,0 +1,67 @@
+{
+    "type": "message",
+    "attachments": [
+        {
+            "contentType": "application/vnd.microsoft.card.adaptive",
+            "contentUrl": null,
+            "content": {
+                "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                "msteams": {
+                    "width": "Full"
+                },
+                "type": "AdaptiveCard",
+                "version": "1.2",
+                "body": [
+                    {
+                        "type": "TextBlock",
+                        "size": "Large",
+                        "weight": "Bolder",
+                        "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>",
+                        "text": "nf-core/testest v${version} - ${runName}",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "spacing": "None",
+                        "text": "Completed at ${dateComplete} (duration: ${duration})",
+                        "isSubtle": true,
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "The command used to launch the workflow was as follows:",
+                        "wrap": true
+                    },
+                    {
+                        "type": "TextBlock",
+                        "text": "${commandLine}",
+                        "isSubtle": true,
+                        "wrap": true
+                    }
+                ],
+                "actions": [
+                    {
+                        "type": "Action.ShowCard",
+                        "title": "Pipeline Configuration",
+                        "card": {
+                            "type": "AdaptiveCard",
+                            "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json",
+                            "body": [
+                                {
+                                    "type": "FactSet",
+                                    "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %>
+                                    ]
+                                }
+                            ]
+                        }
+                    }
+                ]
+            }
+        }
+    ]
+}
diff --git a/assets/slackreport.json b/assets/slackreport.json
@@ -0,0 +1,34 @@
+{
+    "attachments": [
+        {
+            "fallback": "Plain-text summary of the attachment.",
+            "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
+            "author_name": "nf-core/testest ${version} - ${runName}",
+            "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
+            "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
+            "fields": [
+                {
+                    "title": "Command used to launch the workflow",
+                    "value": "```${commandLine}```",
+                    "short": false
+                }
+                <%
+                    if (!success) { %>
+                    ,
+                    {
+                        "title": "Full error message",
+                        "value": "```${errorReport}```",
+                        "short": false
+                    },
+                    {
+                        "title": "Pipeline configuration",
+                        "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
+                        "short": false
+                    }
+                    <% }
+                %>
+            ],
+            "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
+        }
+    ]
+}
diff --git a/conf/test.config b/conf/test.config
@@ -12,7 +12,7 @@
 process {
     resourceLimits = [
         cpus: 2,
-        memory: '4.GB',
+        memory: '8.GB',
         time: '2.h'
     ]
 }
@@ -27,6 +27,6 @@ params {
 
     // Limit resources for github actions
     max_cpus                    = 1
-    max_memory                  = '4.GB'
+    max_memory                  = '8.GB'
     max_time                    = '2.h'
 }