maxulysse · Nov 2, 2026 · Jun 17, 2026 · Jun 17, 2026 · Jun 17, 2026 · Jun 17, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#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, build tool citations from module `meta.yml` with `citationsOnTheFly()` (@maxulysse)
 - [#278](https://github.com/nf-core/seqinspector/pull/278) Back to dev (@maxulysse)
 - [#279](https://github.com/nf-core/seqinspector/pull/279) Exclude CheckQC from individual MultiQC reports to prevent runfolder information from bleeding into other samples' reports (@maxulysse)
 - [#282](https://github.com/nf-core/seqinspector/pull/282) Template update for nf-core/tools v4.1.0 (@maxulysse)

diff --git a/conf/modules.config b/conf/modules.config
@@ -1,14 +1,14 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Config file for defining DSL2 per module options and publishing paths
+Config file for defining DSL2 per module options and publishing paths
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Available keys to override module options:
-        ext.args   = Additional arguments appended to command in module.
-        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
-        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
-        ext.prefix = File name prefix for output files.
+Available keys to override module options:
+ext.args   = Additional arguments appended to command in module.
+ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+ext.prefix = File name prefix for output files.
 ----------------------------------------------------------------------------------------
-*/
+ */
 
 process {
     withName: BBMAP_CLUMPIFY {
@@ -25,19 +25,21 @@ process {
 
     withName: FQ_LINT {
         errorStrategy = {
-            task.exitStatus in ((130..145) + 104) ? 'retry'  :
-            params.continue_with_lint_fail        ? 'ignore' :
-            'finish'
+            task.exitStatus in ((130..145) + 104)
+                ? 'retry'
+                : params.continue_with_lint_fail
+                    ? 'ignore'
+                    : 'finish'
         }
         ext.args      = { params.fq_lint_args }
     }
 
     withName: 'MULTIQC_.*' {
-        ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
+        ext.args = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
     }
 
     withName: PICARD_COLLECTHSMETRICS {
-        ext.args   = { "--TMP_DIR ." }
+        ext.args = { "--TMP_DIR ." }
     }
 
     withName: RIKER_MULTI {

diff --git a/conf/test.config b/conf/test.config
@@ -1,14 +1,14 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
+Nextflow config file for running minimal tests
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines input files and everything required to run a fast and simple pipeline test.
+Defines input files and everything required to run a fast and simple pipeline test.
 
-    Use as follows:
-        nextflow run nf-core/seqinspector -profile test,<docker/singularity> --outdir <OUTDIR>
+Use as follows:
+nextflow run nf-core/seqinspector -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
-*/
+ */
 
 params {
     config_profile_name        = 'Test profile'
@@ -26,7 +26,7 @@ process {
     resourceLimits = [
         cpus: 4,
         memory: '8.GB',
-        time: '1.h'
+        time: '1.h',
     ]
 
     withName: CHECKQC {

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -1,14 +1,14 @@
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running full-size tests
+Nextflow config file for running full-size tests
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Defines input files and everything required to run a full size pipeline test.
+Defines input files and everything required to run a full size pipeline test.
 
-    Use as follows:
-        nextflow run nf-core/seqinspector -profile test_full,<docker/singularity> --outdir <OUTDIR>
+Use as follows:
+nextflow run nf-core/seqinspector -profile test_full,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
-*/
+ */
 
 
 params {

diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
@@ -191,7 +191,6 @@ Tool entries, includes, and references throughout the pipeline must follow alpha
 - `include` statements in workflow files
 - Module invocations within workflows
 - Tool entries in `defineToolsList()` bundles
-- Entries in `toolReferencesMap()`
 - Regex patterns in `nextflow_schema.json`
 - Lists in `docs/usage.md`, `docs/output.md`, `README.md`, and `CITATIONS.md`
 
@@ -209,11 +208,39 @@ The nf-core/seqinspector pipeline has a strong emphasis on a broad spectrum of t
      - If the tool should be part of any pre-defined bundle, update the `help_text` of the `tools_bundle` property to include it in the relevant bundle(s).
 4. Add your tool to the table `Compatibility between tools and data type` in `README.md`.
 5. Add your tool to the tools version table in `README.md` (alphabetical order).
-6. Add your tool to the `toolReferencesMap()` in `subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf` with name, authors, description, and DOI or URL.
+6. Check that the tool entry in the module `meta.yml` has a `publication` block, see [Tool citations](#tool-citations).
 7. Add a citation entry in `CITATIONS.md` (alphabetical order).
 8. Update the metromap (can be found in `assets`) to include your new step.
 9. Update the `CHANGELOG.md` file in the base directory of the pipeline.
 
+### Tool citations
+
+The MultiQC methods description cites tools on the fly with `citationsOnTheFly()` from the nf-core-utils plugin.
+It reads the tools that ran from the `versions` topic and takes their citation from the `tools` entries of every `modules/**/meta.yml`.
+The tool name in the `versions` topic must match the tool key in `meta.yml`.
+
+Each cited tool entry in `meta.yml` should carry a `doi` and a nested `publication` block in Harvard style:
+
+```yaml
+tools:
+  - fastp:
+      doi: "10.1093/bioinformatics/bty560"
+      publication:
+        author: "Chen S., Zhou Y., Chen Y. & Gu J."
+        year: 2018
+        title: "fastp: an ultra-fast all-in-one FASTQ preprocessor"
+        source: "Bioinformatics"
+```
+
+A tool without a `publication` block falls back to its `doi`, then its `homepage`.
+
+The `publication` block is not yet in every upstream nf-core module.
+When an installed module lacks it, add it to the module `meta.yml`, then run `nf-core modules patch <tool>` so the change survives module updates and passes `nf-core pipelines lint`.
+If the module already has a patch, delete the `.diff` file and its `patch` entry in `modules.json`, then run `nf-core modules patch <tool>` again so the new patch covers both changes.
+Open a PR to nf-core/modules to upstream the `publication` block.
+
+MultiQC and MultiQC_SAV run after the `versions` topic is collected, so `workflows/seqinspector.nf` passes them to `citationsOnTheFly()` as extra tools.
+
 ### Things to consider regarding displaying results for a new tool
 
 - If a MultiQC module exist for the tool, start by using the standard settings of the module.

diff --git a/main.nf b/main.nf
@@ -1,19 +1,19 @@
 #!/usr/bin/env nextflow
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    nf-core/seqinspector
+nf-core/seqinspector
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Github : https://github.com/nf-core/seqinspector
-    Website: https://nf-co.re/seqinspector
-    Slack  : https://nfcore.slack.com/channels/seqinspector
+Github : https://github.com/nf-core/seqinspector
+Website: https://nf-co.re/seqinspector
+Slack  : https://nfcore.slack.com/channels/seqinspector
 ----------------------------------------------------------------------------------------
-*/
+ */
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
+IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+ */
 
 include { SEQINSPECTOR             } from './workflows/seqinspector'
 include { PIPELINE_INITIALISATION  } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
@@ -26,9 +26,9 @@ include { defineSubsampleToolsList } from './subworkflows/local/utils_nfcore_seq
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    GENOME PARAMETER VALUES
+GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+ */
 
 params.bwamem2 = getGenomeAttribute('bwamem2')
 params.dict    = getGenomeAttribute('dict')
@@ -37,9 +37,9 @@ params.fasta   = getGenomeAttribute('fasta')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN MAIN WORKFLOW
+RUN MAIN WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+ */
 
 workflow {
 
@@ -194,9 +194,9 @@ output {
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOWS FOR PIPELINE
+NAMED WORKFLOWS FOR PIPELINE
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+ */
 
 //
 // WORKFLOW: Run main analysis pipeline depending on type of input

diff --git a/modules.json b/modules.json
@@ -83,12 +83,14 @@
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "98403d15b0e50edae1f3fec5eae5e24982f1fade",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/multiqc/multiqc.diff"
                     },
                     "multiqcsav": {
                         "branch": "master",
                         "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/multiqcsav/multiqcsav.diff"
                     },
                     "picard/collecthsmetrics": {
                         "branch": "master",
@@ -116,12 +118,14 @@
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/faidx/samtools-faidx.diff"
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "9339809fcb90af8a8b7051e6cd914894d5c52002",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/samtools/index/samtools-index.diff"
                     },
                     "seqfu/stats": {
                         "branch": "master",
@@ -158,25 +162,6 @@
                         "installed_by": ["modules"]
                     }
                 }
-            },
-            "subworkflows": {
-                "nf-core": {
-                    "utils_nextflow_pipeline": {
-                        "branch": "master",
-                        "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfcore_pipeline": {
-                        "branch": "master",
-                        "git_sha": "6ef220fd9252b42fb3c50348bbdbcb6246730686",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfschema_plugin": {
-                        "branch": "master",
-                        "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
-                        "installed_by": ["subworkflows"]
-                    }
-                }
             }
         }
     }

diff --git a/modules/local/rundirparser/meta.yml b/modules/local/rundirparser/meta.yml
@@ -14,6 +14,28 @@ tools:
       documentation: https://github.com/nf-core/seqinspector
       licence:
         - "MIT"
+  - python:
+      description: Python programming language
+      homepage: https://www.python.org/
+      documentation: https://docs.python.org/3/
+      publication:
+        author: "Van Rossum G. & Drake F.L."
+        year: 2009
+        title: "Python 3 Reference Manual"
+        source: "CreateSpace, Scotts Valley, CA"
+      licence:
+        - "PSF-2.0"
+  - pyyaml:
+      description: YAML parser and emitter for Python
+      homepage: https://pyyaml.org/
+      documentation: https://pyyaml.org/wiki/PyYAMLDocumentation
+      publication:
+        author: "Simonov K."
+        year: 2006
+        title: "PyYAML: YAML parser and emitter for Python"
+        source: "https://pyyaml.org/"
+      licence:
+        - "MIT"
 input:
   - - meta:
         type: map

diff --git a/modules/nf-core/checkqc/checkqc.diff b/modules/nf-core/checkqc/checkqc.diff
diff --git a/modules/nf-core/checkqc/meta.yml b/modules/nf-core/checkqc/meta.yml
diff --git a/modules/nf-core/fastqe/fastqe.diff b/modules/nf-core/fastqe/fastqe.diff
diff --git a/modules/nf-core/fastqe/meta.yml b/modules/nf-core/fastqe/meta.yml