Fix bug vib-singlecell-nf/vsn-pipelines#135

processes/reports.nf

@@ -27,14 +27,13 @@ process SC__SCANPY__GENERATE_REPORT {
 		tuple val(sampleId), path("${sampleId}.${reportTitle}.ipynb")
 
 	script:
-		def paramsCopy = params.findAll({!["parseConfig", "parse-config"].contains(it.key)})
 		"""
 		papermill ${ipynb} \
 		    --report-mode \
 			${sampleId}.${reportTitle}.ipynb \
 			-p FILE $adata \
-			-p WORKFLOW_MANIFEST '${toJson(workflow.manifest)}' \
-			-p WORKFLOW_PARAMETERS '${toJson(paramsCopy)}'
+			-p WORKFLOW_MANIFEST '${params.manifestAsJSON}' \
+			-p WORKFLOW_PARAMETERS '${params.paramsAsJSON}'
 		"""
 
 }
@@ -70,7 +69,6 @@ process SC__SCANPY__PARAM_EXPLORE_CLUSTERING_GENERATE_REPORT {
 			val(resolution)
 
 	script:
-		def paramsCopy = params.findAll({!["parseConfig", "parse-config"].contains(it.key)})
 		// In parameter exploration mode, file output needs to be tagged with a unique identitifer because of:
 		// - https://github.com/nextflow-io/nextflow/issues/470
 		stashedParams = [method, resolution]
@@ -81,8 +79,8 @@ process SC__SCANPY__PARAM_EXPLORE_CLUSTERING_GENERATE_REPORT {
 		    --report-mode \
 			${sampleId}.${reportTitle}.${uuid}.ipynb \
 			-p FILE $adata \
-			-p WORKFLOW_MANIFEST '${toJson(workflow.manifest)}' \
-			-p WORKFLOW_PARAMETERS '${toJson(paramsCopy)}'
+			-p WORKFLOW_MANIFEST '${params.manifestAsJSON}' \
+			-p WORKFLOW_PARAMETERS '${params.paramsAsJSON}'
 		"""
 
 }
@@ -119,8 +117,8 @@ process SC__SCANPY__GENERATE_DUAL_INPUT_REPORT {
 		    --report-mode \
 			${sampleId}.${reportTitle}.${isParameterExplorationModeOn ? uuid + "." : ''}ipynb \
 			-p FILE1 $data1 -p FILE2 $data2 \
-			-p WORKFLOW_MANIFEST '${toJson(workflow.manifest)}' \
-			-p WORKFLOW_PARAMETERS '${toJson(paramsCopy)}'
+			-p WORKFLOW_MANIFEST '${params.manifestAsJSON}' \
+			-p WORKFLOW_PARAMETERS '${params.paramsAsJSON}'
 		"""
 
 }