Also allow PDF output; add PDF tests

jch-13 · Feb 7, 2024 · 839cae0 · 839cae0
1 parent b44dea9
commit 839cae0
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Showing 5 changed files with 160 additions and 36 deletions.
diff --git a/modules/nf-core/quartonotebook/main.nf b/modules/nf-core/quartonotebook/main.nf
@@ -17,7 +17,8 @@ process QUARTONOTEBOOK {
     path input_files
 
     output:
-    tuple val(meta), path("*.html")     , emit: html
+    tuple val(meta), path("*.html")     , emit: html, optional: true
+    tuple val(meta), path("*.pdf")      , emit: pdf, optional: true
     tuple val(meta), path("artifacts/*"), emit: artifacts, optional: true
     tuple val(meta), path("params.yml") , emit: params_yaml, optional: true
     path "versions.yml"                 , emit: versions
@@ -39,6 +40,10 @@ process QUARTONOTEBOOK {
     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
 
+    // Get notebook base name and file extension for building final output name
+    def nb_name = notebook.getBaseName()
+    def nb_extension = notebook.getExtension()
+
     // Dump parameters to yaml file.
     // Using a YAML file over using the CLI params because
     //  - No issue with escaping
@@ -77,8 +82,12 @@ process QUARTONOTEBOOK {
     quarto render \\
         ${notebook} \\
         ${render_args} \\
-        ${args} \\
-        --output ${prefix}.html
+        ${args}
+
+    # Change report name to use the prefix and the rendered filetype extension
+    REPORT=\$(find . -name "${nb_name}.*" -not -name "*.${nb_extension}")
+    EXTENSION="\${REPORT/.\\/${nb_name}./}"
+    mv "\$REPORT" "${prefix}.\$EXTENSION"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/quartonotebook/meta.yml b/modules/nf-core/quartonotebook/meta.yml
@@ -50,6 +50,10 @@ output:
       type: file
       description: The HTML report generated by Quarto.
       pattern: "*.html"
+  - pdf:
+      type: file
+      description: The PDF report generated by Quarto.
+      pattern: "*.pdf"
   - artifacts:
       type: file
       description: Artifacts generated by during report execution.

diff --git a/modules/nf-core/quartonotebook/tests/main.nf.test b/modules/nf-core/quartonotebook/tests/main.nf.test
@@ -45,7 +45,7 @@ nextflow_process {
                     [ id:'test' ], // meta map
                     file(params.test_data['generic']['notebooks']['quarto_python'], checkIfExists: true) // Notebook
                 ]
-                input[1] = [] // Parameters
+                input[1] = [:] // Parameters
                 input[2] = [] // Input files
                 """
             }
@@ -166,6 +166,59 @@ nextflow_process {
 
     }
 
+    test("test notebook - pdf - [qmd:r]") {
+
+        config "./pdf.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['generic']['notebooks']['quarto_r'], checkIfExists: true) // Notebook
+                ]
+                input[1] = [:] // parameters
+                input[2] = [] // input files
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.pdf[0][1]).exists() }
+            )
+        }
+
+    }
+
+    test("test notebook - pdf [qmd:python]") {
+
+        config "./pdf.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['generic']['notebooks']['quarto_python'], checkIfExists: true) // Notebook
+                ]
+                input[1] = [:] // Parameters
+                input[2] = [] // Input files
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.pdf[0][1]).exists() }
+            )
+        }
+
+    }
     test("test notebook - stub - [qmd:r]") {
 
         config "./no-parametrization.config"