Init channel-based reports

modules/local/report/render_notebook.nf

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+// Generic process to render a Quarto notebook to HTML
+process RENDER_NOTEBOOK {
+    tag "${report_name}"
+    label 'process_single'
+
+    input:
+    tuple val(report_name), path(notebook), val(data_dir)
+    val project_name
+    val workflow_cmd
+
+    output:
+    path "${report_name}.html"
+
+    script:
+    """
+    ## copy quarto notebook to working directory
+    cp $notebook ${report_name}.qmd
+
+    ## render qmd report to html
+    quarto render ${report_name}.qmd \\
+        -P project_name:${project_name} \\
+        -P workflow_cmd:'${workflow_cmd}' \\
+        -P project_dir:${data_dir} \\
+        -P sample_table:${file(params.samplesheet)} \\
+        --to html
+    """
+
+    stub:
+    """
+    touch ${report_name}.html
+    """
+}

tests/fixtures/test.qmd

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+---
+title: "test notebook"
+format: html
+engine: knitr
+---
+
+```{python}
+print("Hello world!")
+```

tests/modules/local/report/render_notebook.nf.test

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+nextflow_process {
+
+    name "Test RENDER_NOTEBOOK"
+    script "modules/local/report/render_notebook.nf"
+    process "RENDER_NOTEBOOK"
+
+    test("Should render basic notebook") {
+        // note that on Mac M series, jupyter may fail in container
+        // so the test notebook uses knitr engine instead
+
+        tag "basic"
+        tag "notebook"
+
+        when {
+            params {
+                samplesheet = "${projectDir}/tests/fixtures/valid_samplesheet.csv"
+            }
+
+            process {
+                """
+                input[0] = [
+                    "test_notebook",
+                    file("${projectDir}/tests/fixtures/test.qmd"),
+                    "${projectDir}/tests/fixtures"
+                ]
+                input[1] = "TCRtoolkit"
+                input[2] = "nextflow run main.nf"
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert process.out.size() == 1
+        }
+    }
+
+}