From 8ed5a55c8268f46da76a1d1c631e96d051e7491c Mon Sep 17 00:00:00 2001
From: dimalvovs <dmitrijs.lvovs@gmail.com>
Date: Wed, 17 Jun 2026 19:21:21 -0400
Subject: [PATCH 1/3] init channel-based reports

---
 modules/local/report/render_notebook.nf       | 32 ++++++++++++++++
 tests/fixtures/test.qmd                       |  9 +++++
 .../local/report/render_notebook.nf.test      | 38 +++++++++++++++++++
 3 files changed, 79 insertions(+)
 create mode 100644 modules/local/report/render_notebook.nf
 create mode 100644 tests/fixtures/test.qmd
 create mode 100644 tests/modules/local/report/render_notebook.nf.test

diff --git a/modules/local/report/render_notebook.nf b/modules/local/report/render_notebook.nf
new file mode 100644
index 0000000..5b98d4d
--- /dev/null
+++ b/modules/local/report/render_notebook.nf
@@ -0,0 +1,32 @@
+// 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 ${report_name}.html
+    """
+}
diff --git a/tests/fixtures/test.qmd b/tests/fixtures/test.qmd
new file mode 100644
index 0000000..2ab696a
--- /dev/null
+++ b/tests/fixtures/test.qmd
@@ -0,0 +1,9 @@
+---
+title: "test notebook"
+format: html
+engine: knitr
+---
+
+```{python}
+print("Hello world!")
+```
diff --git a/tests/modules/local/report/render_notebook.nf.test b/tests/modules/local/report/render_notebook.nf.test
new file mode 100644
index 0000000..6497f1d
--- /dev/null
+++ b/tests/modules/local/report/render_notebook.nf.test
@@ -0,0 +1,38 @@
+nextflow_process {
+
+    name "Test RENDER_NOTEBOOK"
+    script "modules/local/report/render_notebook.nf"
+    process "RENDER_NOTEBOOK"
+
+    test("Should render basic notebook") {
+        // note that on Mac M series, jupyter may fail in container
+        // so the test notebook uses knitr engine instead
+
+        tag "basic"
+        tag "notebook"
+
+        when {
+            params {
+                samplesheet = "${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
+        }
+    }
+
+}

From 9e398cf7c57b45bf692d30da7ad86f4d4eded675 Mon Sep 17 00:00:00 2001
From: dimalvovs <dmitrijs.lvovs@gmail.com>
Date: Wed, 17 Jun 2026 19:31:53 -0400
Subject: [PATCH 2/3] Apply suggestions from code review

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
---
 tests/modules/local/report/render_notebook.nf.test | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tests/modules/local/report/render_notebook.nf.test b/tests/modules/local/report/render_notebook.nf.test
index 6497f1d..bbbba00 100644
--- a/tests/modules/local/report/render_notebook.nf.test
+++ b/tests/modules/local/report/render_notebook.nf.test
@@ -32,6 +32,11 @@ nextflow_process {
         then {
             assert process.success
             assert process.out.size() == 1
+
+            def html = path(process.out.get(0))
+            assert html.getFileName().toString() == 'test_notebook.html'
+            assert html.exists()
+            assert html.text.contains('Hello world!')
         }
     }
 

From b23a86ec1786bae86145b25ed254f09112806ec2 Mon Sep 17 00:00:00 2001
From: dimalvovs <dmitrijs.lvovs@gmail.com>
Date: Wed, 17 Jun 2026 21:20:08 -0400
Subject: [PATCH 3/3] Revert "Apply suggestions from code review"

This reverts commit 9e398cf7c57b45bf692d30da7ad86f4d4eded675.
---
 tests/modules/local/report/render_notebook.nf.test | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/tests/modules/local/report/render_notebook.nf.test b/tests/modules/local/report/render_notebook.nf.test
index bbbba00..6497f1d 100644
--- a/tests/modules/local/report/render_notebook.nf.test
+++ b/tests/modules/local/report/render_notebook.nf.test
@@ -32,11 +32,6 @@ nextflow_process {
         then {
             assert process.success
             assert process.out.size() == 1
-
-            def html = path(process.out.get(0))
-            assert html.getFileName().toString() == 'test_notebook.html'
-            assert html.exists()
-            assert html.text.contains('Hello world!')
         }
     }