From e82f925751f1d64bb1a7430bb1dae14f73bc7fa5 Mon Sep 17 00:00:00 2001
From: Erik Fasterius <erik.fasterius@outlook.com>
Date: Fri, 16 Aug 2024 12:47:45 +0200
Subject: [PATCH] Update quartonotebook module

---
 modules.json                                  |  2 +-
 .../nf-core/quartonotebook/tests/main.nf.test | 22 +++++++++----------
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/modules.json b/modules.json
index 4bc9e2e..ea627ba 100644
--- a/modules.json
+++ b/modules.json
@@ -17,7 +17,7 @@
                     },
                     "quartonotebook": {
                         "branch": "master",
-                        "git_sha": "93b7e1bf63944488fe77ad490a9de62a73959bed",
+                        "git_sha": "04e1b2340f6cf9cd7b9b06fb7d86da4531714519",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/quartonotebook/quartonotebook.diff"
                     },
diff --git a/modules/nf-core/quartonotebook/tests/main.nf.test b/modules/nf-core/quartonotebook/tests/main.nf.test
index aeec8b1..4fa0ac2 100644
--- a/modules/nf-core/quartonotebook/tests/main.nf.test
+++ b/modules/nf-core/quartonotebook/tests/main.nf.test
@@ -17,7 +17,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['generic']['notebooks']['quarto_r'], checkIfExists: true) // Notebook
+                    file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_r.qmd', checkIfExists: true) // Notebook
                 ]
                 input[1] = [:] // Parameters
                 input[2] = [] // Input files
@@ -44,7 +44,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['generic']['notebooks']['quarto_python'], checkIfExists: true) // Notebook
+                    file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_python.qmd', checkIfExists: true) // Notebook
                 ]
                 input[1] = [] // Parameters
                 input[2] = [] // Input files
@@ -76,10 +76,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['generic']['notebooks']['quarto_r'], checkIfExists: true) // Notebook
+                    file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_r.qmd', checkIfExists: true) // Notebook
                 ]
                 input[1] = [input_filename: "hello.txt", n_iter: 12] // parameters
-                input[2] = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) // Input files
+                input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) // Input files
                 input[3] = [] // Extensions
                 """
             }
@@ -103,10 +103,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['generic']['notebooks']['quarto_python'], checkIfExists: true) // Notebook
+                    file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_python.qmd', checkIfExists: true) // Notebook
                 ]
                 input[1] = [input_filename: "hello.txt", n_iter: 12] // parameters
-                input[2] = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) // Input files
+                input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) // Input files
                 input[3] = [] // Extensions
                 """
             }
@@ -135,10 +135,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) // notebook
+                    file(params.modules_testdata_base_path + 'generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd', checkIfExists: true) // notebook
                 ]
                 input[1] = [input_filename: "hello.txt", n_iter: 12] // parameters
-                input[2] = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) // Input files
+                input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) // Input files
                 input[3] = [] // Extensions
                 """
             }
@@ -162,10 +162,10 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['generic']['notebooks']['ipython_ipynb'], checkIfExists: true) // notebook
+                    file(params.modules_testdata_base_path + 'generic/notebooks/jupyter/ipython_notebook.ipynb', checkIfExists: true) // notebook
                 ]
                 input[1] = [input_filename: "hello.txt", n_iter: 12] // parameters
-                input[2] = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) // Input files
+                input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) // Input files
                 input[3] = [] // Extensions
                 """
             }
@@ -191,7 +191,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test' ], // meta map
-                    file(params.test_data['generic']['notebooks']['quarto_r'], checkIfExists: true) // Notebook
+                    file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_r.qmd', checkIfExists: true) // Notebook
                 ]
                 input[1] = [:] // Parameters
                 input[2] = [] // Input files