nf-core · maxulysse · Jun 17, 2026 · Jun 17, 2026 · Jun 17, 2026 · Jun 17, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -49,6 +49,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#223](https://github.com/nf-core/seqinspector/pull/223) Workflow output for the rest of the pipeline
 - [#235](https://github.com/nf-core/seqinspector/pull/235) Update MultiQC and other dependencies
 - [#237](https://github.com/nf-core/seqinspector/pull/237) Improved citation system to dynamically build tool citations based on selected tools
+- [#241](https://github.com/nf-core/seqinspector/pull/241) Remove vendored nf-core utils subworkflows, use plugin imports from nf-core-utils and nf-schema
 
 ### `Dependencies`
 

diff --git a/modules.json b/modules.json
@@ -146,25 +146,6 @@
                         "installed_by": ["modules"]
                     }
                 }
-            },
-            "subworkflows": {
-                "nf-core": {
-                    "utils_nextflow_pipeline": {
-                        "branch": "master",
-                        "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfcore_pipeline": {
-                        "branch": "master",
-                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfschema_plugin": {
-                        "branch": "master",
-                        "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
-                        "installed_by": ["subworkflows"]
-                    }
-                }
             }
         }
     }

diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml
diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml
diff --git a/modules/nf-core/checkqc/meta.yml b/modules/nf-core/checkqc/meta.yml
diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml
diff --git a/modules/nf-core/fastqe/meta.yml b/modules/nf-core/fastqe/meta.yml
diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml
diff --git a/modules/nf-core/krona/ktimporttaxonomy/meta.yml b/modules/nf-core/krona/ktimporttaxonomy/meta.yml
diff --git a/modules/nf-core/krona/ktupdatetaxonomy/meta.yml b/modules/nf-core/krona/ktupdatetaxonomy/meta.yml
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
diff --git a/modules/nf-core/multiqcsav/meta.yml b/modules/nf-core/multiqcsav/meta.yml
diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml
diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml
diff --git a/modules/nf-core/seqfu/stats/meta.yml b/modules/nf-core/seqfu/stats/meta.yml
diff --git a/modules/nf-core/seqkit/stats/meta.yml b/modules/nf-core/seqkit/stats/meta.yml
diff --git a/modules/nf-core/sequali/meta.yml b/modules/nf-core/sequali/meta.yml
diff --git a/nextflow.config b/nextflow.config
@@ -456,7 +456,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-core-utils@0.4.0' // nf-core-utils is a collection of utilities for Nextflow pipelines
+    id 'nf-core-utils@0.6.0' // nf-core-utils is a collection of utilities for Nextflow pipelines
     id 'nf-schema@2.6.1'     // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 

diff --git a/nf-test.config b/nf-test.config
@@ -34,6 +34,6 @@ config {
     // load the necessary plugins
     plugins {
         load "nft-bam@0.4.0"
-        load "nft-utils@0.0.9"
+        load "nft-utils@1.0.0"
     }
 }