fix: DSL2 optional-output syntax for Nextflow 25.x + clamp version

modules/local/msstats/main.nf

@@ -15,7 +15,7 @@ process MSSTATS {
     output:
     // The generation of the PDFs from MSstats are very unstable, especially with auto-contrasts.
     // And users can easily fix anything based on the csv and the included script -> make optional
-    path "*.pdf" optional true
+    path "*.pdf", optional: true
     path "*.csv", emit: msstats_csv
     path "*.log", emit: log
     path "versions.yml" , emit: version

modules/local/msstatstmt/main.nf

@@ -15,7 +15,7 @@ process MSSTATSTMT {
     output:
     // The generation of the PDFs from MSstatsTMT are very unstable, especially with auto-contrasts.
     // And users can easily fix anything based on the csv and the included script -> make optional
-    path "*.pdf" optional true
+    path "*.pdf", optional: true
     path "*.csv", emit: msstats_csv
     path "*.log"
     path "versions.yml" , emit: version

modules/local/openms/proteomicslfq/main.nf

@@ -17,14 +17,14 @@ process PROTEOMICSLFQ {
     output:
     path "${expdes.baseName}_openms.mzTab", emit: out_mztab
     path "${expdes.baseName}_openms.consensusXML", emit: out_consensusXML
-    path "*msstats_in.csv", emit: out_msstats optional true
-    path "*triqler_in.tsv", emit: out_triqler optional true
-    path "debug_mergedIDs.idXML", emit: debug_mergedIDs optional true
-    path "debug_mergedIDs_inference.idXML", emit: debug_mergedIDs_inference optional true
-    path "debug_mergedIDsGreedyResolved.idXML", emit: debug_mergedIDsGreedyResolved optional true
-    path "debug_mergedIDsGreedyResolvedFDR.idXML", emit: debug_mergedIDsGreedyResolvedFDR optional true
-    path "debug_mergedIDsGreedyResolvedFDRFiltered.idXML", emit: debug_mergedIDsGreedyResolvedFDRFiltered optional true
-    path "debug_mergedIDsFDRFilteredStrictlyUniqueResolved.idXML", emit: debug_mergedIDsFDRFilteredStrictlyUniqueResolved optional true
+    path "*msstats_in.csv", emit: out_msstats, optional: true
+    path "*triqler_in.tsv", emit: out_triqler, optional: true
+    path "debug_mergedIDs.idXML", emit: debug_mergedIDs, optional: true
+    path "debug_mergedIDs_inference.idXML", emit: debug_mergedIDs_inference, optional: true
+    path "debug_mergedIDsGreedyResolved.idXML", emit: debug_mergedIDsGreedyResolved, optional: true
+    path "debug_mergedIDsGreedyResolvedFDR.idXML", emit: debug_mergedIDsGreedyResolvedFDR, optional: true
+    path "debug_mergedIDsGreedyResolvedFDRFiltered.idXML", emit: debug_mergedIDsGreedyResolvedFDRFiltered, optional: true
+    path "debug_mergedIDsFDRFilteredStrictlyUniqueResolved.idXML", emit: debug_mergedIDsFDRFilteredStrictlyUniqueResolved, optional: true
     path "*.log", emit: log
     path "versions.yml", emit: version
 

nextflow.config

@@ -443,7 +443,7 @@ manifest {
     homePage        = 'https://github.com/nf-core/quantms'
     description     = """Quantitative Mass Spectrometry nf-core workflow"""
     mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
+    nextflowVersion = '!>=25.04.0'
     version         = '1.2.0'
     doi             = '10.5281/zenodo.7754148'
 }