Merge pull request #57 from seqeralabs/viralrecon_config_slurper

fix: check if fusion is enabled via the Platform API

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

modules/local/seqera_runs_dump/functions.nf

@@ -2,6 +2,7 @@
 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) {
@@ -49,8 +50,10 @@ Map getRunMetadata(meta, log, api_endpoint, trustStorePath, trustStorePassword)
             def workflowResponse = client.get(path: "/workflow/${runId}", query: ["workspaceId":workspaceId], headers: authHeader)
             if (workflowResponse.statusCode == 200) {
                 def metaMap = workflowResponse?.json?.workflow?.subMap("runName", "workDir", "projectName")
-                def config = new ConfigSlurper().parse( workflowResponse?.json?.workflow?.configText )
-                metaMap.fusion =  config.fusion.enabled
+                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 ?: [:]
             }

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             = ''
 }