nf-core · jonasscheid · Jan 8, 2026 · Jan 8, 2026 · Jan 8, 2026
diff --git a/modules/nf-core/gunzip/tests/main.nf.test b/modules/nf-core/gunzip/tests/main.nf.test
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
diff --git a/modules/nf-core/openms/filefilter/tests/main.nf.test b/modules/nf-core/openms/filefilter/tests/main.nf.test
diff --git a/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test
diff --git a/modules/nf-core/openms/idmerger/tests/main.nf.test b/modules/nf-core/openms/idmerger/tests/main.nf.test
diff --git a/modules/nf-core/openms/idripper/tests/main.nf.test b/modules/nf-core/openms/idripper/tests/main.nf.test
diff --git a/modules/nf-core/openms/peptideindexer/tests/main.nf.test b/modules/nf-core/openms/peptideindexer/tests/main.nf.test
diff --git a/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test
diff --git a/subworkflows/local/map_alignment/main.nf b/subworkflows/local/map_alignment/main.nf
@@ -14,7 +14,7 @@ workflow MAP_ALIGNMENT {
         merge_meta_map
 
     main:
-        ch_versions = Channel.empty()
+        ch_versions = channel.empty()
 
         // Compute group-wise alignment rt transformation
         OPENMS_MAPALIGNERIDENTIFICATION( ch_runs_to_be_aligned )

diff --git a/subworkflows/local/prepare_spectra/main.nf b/subworkflows/local/prepare_spectra/main.nf
@@ -14,7 +14,7 @@ workflow PREPARE_SPECTRA {
         ch_samplesheet
 
     main:
-        ch_versions = Channel.empty()
+        ch_versions = channel.empty()
 
         ch_samplesheet
         .branch {

diff --git a/subworkflows/local/process_feature/main.nf b/subworkflows/local/process_feature/main.nf
@@ -11,7 +11,7 @@ workflow PROCESS_FEATURE {
         ch_runs_to_be_quantified
 
     main:
-        ch_versions = Channel.empty()
+        ch_versions = channel.empty()
 
         // Quantify identifications using targeted feature extraction
         OPENMS_FEATUREFINDERIDENTIFICATION(ch_runs_to_be_quantified).featurexml

diff --git a/subworkflows/local/quant/main.nf b/subworkflows/local/quant/main.nf
@@ -25,7 +25,7 @@ workflow QUANT {
         mzml
 
     main:
-        ch_versions = Channel.empty()
+        ch_versions = channel.empty()
         // Split post-percolator idXML files and manipulate such that we end up with [meta_run1, idxml_run1] [meta_run2, idxml_run2] ...
         // We need to make sure that the order of the runs is the same as in the mzml files since IDRipper always sorts the runs
         // (and nextflow does not guarantee the order of the maps in merged_meta_map)

diff --git a/subworkflows/local/rescore/main.nf b/subworkflows/local/rescore/main.nf
@@ -28,7 +28,7 @@ workflow RESCORE {
         ch_multiqc_files
 
     main:
-        ch_versions = Channel.empty()
+        ch_versions = channel.empty()
 
     // Compute features via ms2rescore
     MS2RESCORE(ch_merged_runs)

diff --git a/subworkflows/local/speclib/main.nf b/subworkflows/local/speclib/main.nf
@@ -21,7 +21,7 @@ workflow SPECLIB {
         mzml
 
     main:
-        ch_versions = Channel.empty()
+        ch_versions = channel.empty()
 
     // Load unimod tables (Future:)
     unimod = file("$projectDir/assets/250120_unimod_tables.xml", checkIfExists: true)

diff --git a/subworkflows/local/utils_nfcore_mhcquant_pipeline/main.nf b/subworkflows/local/utils_nfcore_mhcquant_pipeline/main.nf
@@ -114,7 +114,7 @@ workflow PIPELINE_INITIALISATION {
     //
 
     if (params.fasta) {
-        Channel.fromPath(params.fasta, checkIfExists: true)
+        channel.fromPath(params.fasta, checkIfExists: true)
             .map { fasta -> [[id:fasta.getBaseName()], fasta] }
             .set { ch_fasta }
 

diff --git a/workflows/mhcquant.nf b/workflows/mhcquant.nf
@@ -57,8 +57,8 @@ workflow MHCQUANT {
     ch_fasta       // channel: reference database read in from --fasta
 
     main:
-    ch_versions = Channel.empty()
-    ch_multiqc_files = Channel.empty()
+    ch_versions = channel.empty()
+    ch_multiqc_files = channel.empty()
 
     // Prepare spectra files (Decompress archives, convert to mzML, centroid if specified)
     PREPARE_SPECTRA(ch_samplesheet)
@@ -233,7 +233,7 @@ workflow MHCQUANT {
     //
     // Collate and save software versions
     //
-    def topic_versions = Channel.topic("versions")
+    def topic_versions = channel.topic("versions")
         .distinct()
         .branch { entry ->
             versions_file: entry instanceof Path