Merge pull request #58 from seqeralabs/dev

Dev -> Main for 0.4.0 release
seqeralabs · Jul 26, 2024 · 3831d1f · 3831d1f
2 parents c9aec68 + a98423a
commit 3831d1f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,22 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[0.4.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.4.0)] - 2024-07-26
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Friederike Hanssen](https://github.com/FriederikeHanssen)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+[PR #52](https://github.com/seqeralabs/nf-aggregate/pull/52) - Organise results folder structure by pipeline
+[PR #53](https://github.com/seqeralabs/nf-aggregate/pull/53) - Throw exception and terminate workflow in case config can't be read
+[PR #57](https://github.com/seqeralabs/nf-aggregate/pull/57) - Check if fusion is enabled via the Platform API
+
 ## [[0.3.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.3.0)] - 2024-07-01
 
 ### Credits

diff --git a/modules/local/seqera_runs_dump/functions.nf b/modules/local/seqera_runs_dump/functions.nf
@@ -1,6 +1,8 @@
 @Grab('com.github.groovy-wslite:groovy-wslite:1.1.2;transitive=false')
 import wslite.rest.RESTClient
 import groovy.json.JsonSlurper
+import nextflow.exception.ProcessException
+import groovy.json.JsonBuilder
 
 // Set system properties for custom Java trustStore
 def setTrustStore(trustStorePath, trustStorePassword) {
@@ -47,9 +49,11 @@ Map getRunMetadata(meta, log, api_endpoint, trustStorePath, trustStorePassword)
         if (workspaceId) {
             def workflowResponse = client.get(path: "/workflow/${runId}", query: ["workspaceId":workspaceId], headers: authHeader)
             if (workflowResponse.statusCode == 200) {
-                metaMap = workflowResponse?.json?.workflow?.subMap("runName", "workDir", "projectName")
-                config = new ConfigSlurper().parse( workflowResponse?.json?.workflow?.configText )
-                metaMap.fusion =  config.fusion.enabled
+                def metaMap = workflowResponse?.json?.workflow?.subMap("runName", "workDir", "projectName")
+                def configText = new JsonBuilder(workflowResponse?.json?.workflow?.configText)
+                def pattern = /fusion\s*\{\\n\s*enabled\s*=\s*true/
+                def matcher = configText.toPrettyString() =~ pattern
+                metaMap.fusion = matcher.find()
 
                 return metaMap ?: [:]
             }
@@ -60,12 +64,15 @@ Map getRunMetadata(meta, log, api_endpoint, trustStorePath, trustStorePassword)
             ↳ Status code ${ex.response?.statusCode} returned from request to ${ex.request?.url} (authentication headers excluded)
         """.stripIndent()
         log.error "Exception: ${ex.message}", ex
+        throw new ProcessException("Failed to get workflow details for workflow ${runId} in workspace ${meta.workspace}", ex)
     } catch (Exception ex) {
         log.warn """
         An error occurred while getting workflow details for workflow ${runId} in workspace ${meta.workspace}:
             ↳ ${ex.message}
         """.stripIndent()
         log.error "Exception: ${ex.message}", ex
+        throw new ProcessException("Failed to get workflow details for workflow ${runId} in workspace ${meta.workspace}", ex)
+
     }
     return [:]
 }
diff --git a/modules/local/seqera_runs_dump/tests/main.nf.test.snap b/modules/local/seqera_runs_dump/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "Should run without failures": {
         "content": [
             [
-                "service-info.json:md5,108f149aafa287bb56d715c0c7ee0359",
+                "service-info.json:md5,72586e82ad2064d1a90008c7956d80d8",
                 "workflow-load.json:md5,4f02d5a24ab89aa648cd4346785c8f2c",
                 "workflow-metadata.json:md5,b37b4faeddf283a2c44cbe4000e4ab6e",
                 "workflow-metrics.json:md5,13a5b5d7447fad4a8baa053d1abf85e5",
@@ -13,8 +13,8 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.2"
         },
-        "timestamp": "2024-05-20T15:32:40.565622058"
+        "timestamp": "2024-07-25T10:21:06.447483"
     }
 }
diff --git a/nextflow.config b/nextflow.config
@@ -222,6 +222,6 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.10.0'
     defaultBranch   = 'main'
-    version         = '0.3.0'
+    version         = '0.4.0'
     doi             = ''
 }
diff --git a/workflows/nf_aggregate/main.nf b/workflows/nf_aggregate/main.nf
@@ -21,7 +21,7 @@ workflow NF_AGGREGATE {
     skip_multiqc              //     val: Skip MultiQC
     java_truststore_path      //     val: Path to java truststore if using private certs
     java_truststore_password  //     val: Password for java truststore if using private certs
-    
+
     main:
 
     ch_versions = Channel.empty()
@@ -30,6 +30,7 @@ workflow NF_AGGREGATE {
     //
     // MODULE: Fetch run information via the Seqera CLI
     //
+
     SEQERA_RUNS_DUMP (
         ids,
         seqera_api_endpoint,