Remove non-standard ext keys and model after quartonotebook

modules/nf-core/rmarkdownnotebook/main.nf

@@ -1,5 +1,3 @@
-include { dump_params_yml; indent_code_block } from "./parametrize"
-
 process RMARKDOWNNOTEBOOK {
     tag "$meta.id"
     label 'process_low'
@@ -18,93 +16,34 @@ process RMARKDOWNNOTEBOOK {
     path input_files
 
     output:
-    tuple val(meta), path("*.html")              , emit: report
-    tuple val(meta), path("*.parameterised.Rmd") , emit: parameterised_notebook, optional: true
-    tuple val(meta), path("artifacts/*")         , emit: artifacts, optional: true
-    tuple val(meta), path("session_info.log")    , emit: session_info
-    path  "versions.yml"                         , emit: versions
+    tuple val(meta), path("*.html")             , emit: report
+    tuple val(meta), path("*.parameterised.Rmd"), emit: parameterised_notebook, optional: true
+    tuple val(meta), path("artifacts/*")        , emit: artifacts, optional: true
+    tuple val(meta), path("session_info.log")   , emit: session_info
+    path  "versions.yml"                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     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
+    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 = ""
-    if (parametrize) {
-        nb_params = [:]
-        if (implicit_params) {
-            nb_params["cpus"] = task.cpus
-            nb_params["artifact_dir"] = "artifacts"
-            nb_params["input_dir"] = "./"
-        }
-        if (meta_params) {
-            nb_params["meta"] = meta
-        }
-        nb_params += parameters
-        params_cmd = dump_params_yml(nb_params)
-        render_cmd = """\
-            params = yaml::read_yaml('.params.yml')
-
-            # Instead of rendering with params, produce a version of the R
-            # markdown with param definitions set, so the notebook itself can
-            # be reused
-            rmd_content <- readLines('${prefix}.Rmd')
-
-            # Extract YAML content between the first two '---'
-            start_idx <- which(rmd_content == "---")[1]
-            end_idx <- which(rmd_content == "---")[2]
-            rmd_yaml_content <- paste(rmd_content[(start_idx+1):(end_idx-1)], collapse = "\\n")
-            rmd_params <- yaml::yaml.load(rmd_yaml_content)
-
-            # Override the params
-            rmd_params[['params']] <- modifyList(rmd_params[['params']], params)
-
-            # Recursive function to add 'value' to list elements, except for top-level
-            add_value_recursively <- function(lst, is_top_level = FALSE) {
-                if (!is.list(lst)) {
-                    return(lst)
-                }
-
-                lst <- lapply(lst, add_value_recursively)
-                if (!is_top_level) {
-                    lst <- list(value = lst)
-                }
-                return(lst)
-            }
-
-            # Reformat nested lists under 'params' to have a 'value' key recursively
-            rmd_params[['params']] <- add_value_recursively(rmd_params[['params']], is_top_level = TRUE)
-
-            # Convert back to YAML string
-            updated_yaml_content <- as.character(yaml::as.yaml(rmd_params))
-
-            # Remove the old YAML content
-            rmd_content <- rmd_content[-((start_idx+1):(end_idx-1))]
-
-            # Insert the updated YAML content at the right position
-            rmd_content <- append(rmd_content, values = unlist(strsplit(updated_yaml_content, split = "\\n")), after = start_idx)
-
-            writeLines(rmd_content, '${prefix}.parameterised.Rmd')
-
-            # Render based on the updated file
-            rmarkdown::render('${prefix}.parameterised.Rmd', output_file='${prefix}.html', envir = new.env())
-        """
-    } else {
-        render_cmd = "rmarkdown::render('${prefix}.Rmd', output_file='${prefix}.html')"
-    }
-
+    def yamlBuilder = new groovy.yaml.YamlBuilder()
+    yamlBuilder.call(notebook_parameters)
+    def yaml_content = yamlBuilder.toString().tokenize('\n').join("\n    ")
     """
-    # Dump .params.yml heredoc (section will be empty if parametrization is disabled)
-    ${indent_code_block(params_cmd, 4)}
+    # Dump parameters to yaml file
+    cat <<- END_YAML_PARAMS > params.yml
+    ${yaml_content}
+    END_YAML_PARAMS
 
     # Create output directory
     mkdir artifacts
@@ -122,8 +61,52 @@ process RMARKDOWNNOTEBOOK {
 
     # Render notebook
     Rscript - <<EOF
-        ${indent_code_block(render_cmd, 8)}
-        writeLines(capture.output(sessionInfo()), "session_info.log")
+    params = yaml::read_yaml('params.yml')
+
+    # Instead of rendering with params, produce a version of the R
+    # markdown with param definitions set, so the notebook itself can
+    # be reused
+    rmd_content <- readLines('${prefix}.Rmd')
+
+    # Extract YAML content between the first two '---'
+    start_idx <- which(rmd_content == "---")[1]
+    end_idx <- which(rmd_content == "---")[2]
+    rmd_yaml_content <- paste(rmd_content[(start_idx+1):(end_idx-1)], collapse = "\\n")
+    rmd_params <- yaml::yaml.load(rmd_yaml_content)
+
+    # Override the params
+    rmd_params[['params']] <- modifyList(rmd_params[['params']], params)
+
+    # Recursive function to add 'value' to list elements, except for top-level
+    add_value_recursively <- function(lst, is_top_level = FALSE) {
+        if (!is.list(lst)) {
+            return(lst)
+        }
+
+        lst <- lapply(lst, add_value_recursively)
+        if (!is_top_level) {
+            lst <- list(value = lst)
+        }
+        return(lst)
+    }
+
+    # Reformat nested lists under 'params' to have a 'value' key recursively
+    rmd_params[['params']] <- add_value_recursively(rmd_params[['params']], is_top_level = TRUE)
+
+    # Convert back to YAML string
+    updated_yaml_content <- as.character(yaml::as.yaml(rmd_params))
+
+    # Remove the old YAML content
+    rmd_content <- rmd_content[-((start_idx+1):(end_idx-1))]
+
+    # Insert the updated YAML content at the right position
+    rmd_content <- append(rmd_content, values = unlist(strsplit(updated_yaml_content, split = "\\n")), after = start_idx)
+
+    writeLines(rmd_content, '${prefix}.parameterised.Rmd')
+
+    # Render based on the updated file
+    rmarkdown::render('${prefix}.parameterised.Rmd', output_file='${prefix}.html', envir = new.env())
+    writeLines(capture.output(sessionInfo()), "session_info.log")
     EOF
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/rmarkdownnotebook/meta.yml

@@ -10,24 +10,9 @@ tools:
       homepage: https://rmarkdown.rstudio.com/
       documentation: https://rmarkdown.rstudio.com/lesson-1.html
       tool_dev_url: https://github.com/rstudio/rmarkdown
-      licence: ["GPL-3"]
+      licence:
+        - "GPL-3"
       identifier: ""
-params:
-  - parametrize:
-      type: boolean
-      description: If true, parametrize the notebook
-  - implicit_params:
-      type: boolean
-      description: |
-        If true (default), include the implicit params
-          * `input_dir`, which points to the directory containing the files added via `input_files`,
-          * `artifact_dir`, which points to the directory where the notebook should place output files, and
-          * `cpus`, which contains the value of ${task.cpus}
-  - meta_params:
-      type: boolean
-      description: |
-        If true, include a parameter `meta` which contains the information specified
-        via the `meta` input channel.
 input:
   - - meta:
         type: map
@@ -39,7 +24,7 @@ input:
         description: Rmarkdown file
         pattern: "*.{Rmd}"
         ontologies:
-          - edam: http://edamontology.org/format_4000 # R markdown
+          - edam: http://edamontology.org/format_4000
   - parameters:
       type: map
       description: |
@@ -73,7 +58,7 @@ output:
           description: Parameterised Rmarkdown file
           pattern: "*.parameterised.Rmd"
           ontologies:
-            - edam: http://edamontology.org/format_4000 # R markdown
+            - edam: http://edamontology.org/format_4000
   artifacts:
     - - meta:
           type: map
@@ -102,7 +87,7 @@ 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/rmarkdownnotebook/tests/main.nf.test

@@ -11,9 +11,6 @@ nextflow_process {
     test("test_rmarkdownnotebook") {
 
         when {
-            params{
-                module_args = false
-            }
             process {
                 """
                 input[0] = [
@@ -43,16 +40,13 @@ nextflow_process {
     test("test_rmarkdownnotebook_parametrize") {
 
         when {
-            params{
-                module_args = true
-            }
             process {
                 """
                 input[0] = [
                     [ id:'test_rmd' ],
                     file(params.modules_testdata_base_path + 'generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd', checkIfExists: true)
                 ]
-                input[1] = [input_filename: "hello.txt", n_iter: 12]
+                input[1] = [input_filename: "hello.txt", n_iter: 12, input_dir: "./"]
                 input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true)
                 """
             }
@@ -77,9 +71,6 @@ nextflow_process {
         options "-stub"
 
         when {
-            params{
-                module_args = false
-            }
             process {
                 """
                 input[0] = [

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

@@ -3,7 +3,12 @@
         "content": [
             "test_rmd.html",
             [
-
+                [
+                    {
+                        "id": "test_rmd"
+                    },
+                    "test_rmd.parameterised.Rmd:md5,54d7d6576e3d8432effd8f449d018604"
+                ]
             ],
             [
 
@@ -15,9 +20,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2025-02-17T12:51:28.269874594"
+        "timestamp": "2026-03-18T13:10:53.025617"
     },
     "test_rmarkdownnotebook_parametrize": {
         "content": [
@@ -27,16 +32,11 @@
                     {
                         "id": "test_rmd"
                     },
-                    "test_rmd.parameterised.Rmd:md5,59e184e50aadb66a821a2acce6a7c27c"
+                    "test_rmd.parameterised.Rmd:md5,841b2c0d847c191b92547ae5b77e09ab"
                 ]
             ],
             [
-                [
-                    {
-                        "id": "test_rmd"
-                    },
-                    "artifact.txt:md5,b10a8db164e0754105b7a99be72e3fe5"
-                ]
+
             ],
             "session_info.log",
             [
@@ -45,9 +45,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nextflow": "25.10.4"
         },
-        "timestamp": "2025-02-17T12:51:36.802094082"
+        "timestamp": "2026-03-18T13:10:59.388999"
     },
     "test_rmarkdownnotebook - stub": {
         "content": [

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

@@ -1,3 +0,0 @@
-process {
-    ext.parametrize = params.module_args
-}