Remove non-standard ext keys from jupyternotebook

modules/nf-core/jupyternotebook/main.nf

@@ -14,6 +14,7 @@ process JUPYTERNOTEBOOK {
     tuple val(meta), path(notebook)
     val parameters
     path input_files
+    val kernel_
 
     output:
     tuple val(meta), path("*.html")    , emit: report
@@ -25,38 +26,25 @@ process JUPYTERNOTEBOOK {
 
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def parametrize = (task.ext.parametrize == null) ?  true : task.ext.parametrize
-    def implicit_params = (task.ext.implicit_params == null) ? true : task.ext.implicit_params
-    def meta_params = (task.ext.meta_params == null) ? true : task.ext.meta_params
-    def kernel   = task.ext.kernel ?: '-'
+    def kernel   = kernel_ ?: '-'
+    // Implicit parameters can be overwritten by supplying a value with parameters
+    notebook_parameters = [
+        meta: meta,
+        cpus: task.cpus,
+    ] + (parameters ?: [:])
 
     // Dump parameters to yaml file.
     // Using a yaml file over using the CLI params because
     //  * no issue with escaping
     //  * allows to pass nested maps instead of just single values
-    def params_cmd = ""
-    def render_cmd = ""
-    def meta_string = meta.collect { key, value -> "${key}: ${value}" }.join('\n')
-    def params_string = parameters.collect { key, value -> "${key}: ${value}" }.join('\n')
-    if (parametrize) {
-        if (implicit_params) {
-            params_cmd += 'echo cpus: ' + task.cpus + ' >> ./.params.yml \n'
-            params_cmd += 'echo "artifact_dir: artifacts"  >> ./.params.yml \n'
-            params_cmd += 'echo "input_dir: ./"  >> ./.params.yml \n'
-        }
-        if (meta_params) {
-            params_cmd += 'echo "' + meta_string + '" >> ./.params.yml \n'
-        }
-        params_cmd += 'echo "' + params_string + '" >> ./.params.yml'
-        render_cmd = "papermill -f .params.yml"
-    } else {
-        render_cmd = "papermill"
-    }
+    def yamlBuilder = new groovy.yaml.YamlBuilder()
+    yamlBuilder.call(notebook_parameters)
+    def yaml_content = yamlBuilder.toString().tokenize('\n').join("\n    ")
     """
-    set -o pipefail
-
-    # write .params.yml file if required
-    $params_cmd
+    # Dump parameters to yaml file
+    cat <<- END_YAML_PARAMS > params.yml
+    ${yaml_content}
+    END_YAML_PARAMS
 
     # Create output directory
     mkdir artifacts
@@ -72,7 +60,7 @@ process JUPYTERNOTEBOOK {
 
     # Convert notebook to ipynb using jupytext, execute using papermill, convert using nbconvert
     jupytext --to notebook --output - --set-kernel ${kernel} ${notebook} > ${notebook}.ipynb
-    ${render_cmd} ${notebook}.ipynb ${notebook}.executed.ipynb
+    papermill -f params.yml ${notebook}.ipynb ${notebook}.executed.ipynb
     jupyter nbconvert --stdin --to html --output ${prefix}.html < ${notebook}.executed.ipynb
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/jupyternotebook/meta.yml

@@ -15,21 +15,24 @@ tools:
       homepage: https://github.com/mwouts/jupytext/
       documentation: https://jupyter.org/documentation
       tool_dev_url: https://github.com/mwouts/jupytext/
-      license: ["MIT"]
+      license:
+        - "MIT"
       identifier: ""
   - papermill:
       description: Parameterize, execute, and analyze notebooks
       homepage: https://github.com/nteract/papermill
       documentation: http://papermill.readthedocs.io/en/latest/
       tool_dev_url: https://github.com/nteract/papermill
-      license: ["BSD 3-clause"]
+      license:
+        - "BSD 3-clause"
       identifier: ""
   - nbconvert:
       description: Parameterize, execute, and analyze notebooks
       homepage: https://nbconvert.readthedocs.io/en/latest/
       documentation: https://nbconvert.readthedocs.io/en/latest/
       tool_dev_url: https://github.com/jupyter/nbconvert
-      license: ["BSD 3-clause"]
+      license:
+        - "BSD 3-clause"
       identifier: ""
 input:
   - - meta:
@@ -42,8 +45,8 @@ input:
         description: Jupyter notebook or jupytext representation thereof
         pattern: "*.{ipynb,py,md,Rmd,myst}"
         ontologies:
-          - edam: http://edamontology.org/format_3996 # Python script
-          - edam: http://edamontology.org/format_4000 # R markdown
+          - edam: http://edamontology.org/format_3996
+          - edam: http://edamontology.org/format_4000
   - parameters:
       type: map
       description: |
@@ -54,6 +57,9 @@ input:
       description: One or multiple files serving as input data for the notebook.
       pattern: "*"
       ontologies: []
+  - kernel_:
+      type: string
+      description: Name of the kernel to use.
 output:
   report:
     - - meta:
@@ -82,7 +88,7 @@ output:
         description: File containing software versions
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
 authors:
   - "@grst"
 maintainers:

modules/nf-core/jupyternotebook/tests/main.nf.test

@@ -12,15 +12,13 @@ nextflow_process {
     test("generic - md") {
 
         when {
-            params {
-                module_args = ['parametrize':false]
-            }
             process {
                 """
                 input[0] = [[id:'test_jupyter'],
                     file(params.modules_testdata_base_path + 'generic/notebooks/jupyter/ipython_notebook.md', checkIfExists:true)]
                 input[1] = [:]
                 input[2] = []
+                input[3] = ''
                 """
             }
         }
@@ -39,15 +37,13 @@ nextflow_process {
     test("generic - md - parametrize") {
 
         when {
-            params {
-                module_args = ['parametrize':true]
-            }
             process {
                 """
                 input[0] = [[id:'test_jupyter'],
                     file(params.modules_testdata_base_path + 'generic/notebooks/jupyter/ipython_notebook.md', checkIfExists:true)]
                 input[1] = [input_filename:"hello.txt", n_iter:12]
                 input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists:true)
+                input[3] = ''
                 """
             }
         }
@@ -68,15 +64,13 @@ nextflow_process {
 
 
         when {
-            params {
-                module_args = ['parametrize':true]
-            }
             process {
                 """
                 input[0] = [[id:'test_jupyter'],
                     file(params.modules_testdata_base_path + 'generic/notebooks/jupyter/ipython_notebook.ipynb', checkIfExists:true)]
                 input[1] = [input_filename:"hello.txt", n_iter:12]
                 input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists:true)
+                input[3] = ''
                 """
             }
         }
@@ -98,15 +92,13 @@ nextflow_process {
         options "-stub"
 
         when {
-            params {
-                module_args = ['parametrize':false]
-            }
             process {
                 """
                 input[0] = [[id:'test_jupyter'],
                     file(params.modules_testdata_base_path + 'generic/notebooks/jupyter/ipython_notebook.md', checkIfExists:true)]
                 input[1] = [:]
                 input[2] = []
+                input[3] = ''
                 """
             }
         }

modules/nf-core/jupyternotebook/tests/main.nf.test.snap

@@ -9,19 +9,19 @@
                         "id": "test_jupyter"
                     },
                     [
-                        "artifact.txt:md5,8ddd8be4b179a529afa5f2ffae4b9858"
+
                     ]
                 ]
             ],
             [
-                "versions.yml:md5,d117eb87cb1392fe15e7b46ba822825a"
+                "versions.yml:md5,fc2a7a3269fbae7ce3d9c8a17b91de01"
             ]
         ],
+        "timestamp": "2026-03-13T20:41:47.791483035",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
-        },
-        "timestamp": "2025-05-30T11:35:17.89341504"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "generic - md - stub": {
         "content": [
@@ -70,11 +70,11 @@
                 ]
             }
         ],
+        "timestamp": "2025-05-29T14:34:50.943899122",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2025-05-29T14:34:50.943899122"
+        }
     },
     "generic - md - parametrize": {
         "content": [
@@ -86,19 +86,19 @@
                         "id": "test_jupyter"
                     },
                     [
-                        "artifact.txt:md5,8ddd8be4b179a529afa5f2ffae4b9858"
+
                     ]
                 ]
             ],
             [
-                "versions.yml:md5,d117eb87cb1392fe15e7b46ba822825a"
+                "versions.yml:md5,fc2a7a3269fbae7ce3d9c8a17b91de01"
             ]
         ],
+        "timestamp": "2026-03-13T20:41:31.036482511",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
-        },
-        "timestamp": "2025-05-30T11:34:58.272377123"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "generic - md": {
         "content": [
@@ -108,10 +108,10 @@
                 "versions.yml:md5,fc2a7a3269fbae7ce3d9c8a17b91de01"
             ]
         ],
+        "timestamp": "2025-05-30T11:28:28.193453013",
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.6"
-        },
-        "timestamp": "2025-05-30T11:28:28.193453013"
+        }
     }
 }

modules/nf-core/jupyternotebook/tests/nextflow.config

@@ -1,5 +0,0 @@
-process {
-    withName: "JUPYTERNOTEBOOK" {
-        ext = params.module_args
-    }
-}