From ec57c62d05efe90416bde2827c1d7cf1f76cfd87 Mon Sep 17 00:00:00 2001
From: alessiovignoli <alessio.vignoli3@studio.unibo.it>
Date: Fri, 7 Jun 2024 12:04:53 +0200
Subject: [PATCH] debugging nf-test input file not found

---
 nf-test.config            |  2 +-
 tests/handle_data.nf.test | 29 +++++++++++++++++++++++++++++
 tests/main.nf.test        | 28 ----------------------------
 3 files changed, 30 insertions(+), 29 deletions(-)
 create mode 100644 tests/handle_data.nf.test
 delete mode 100644 tests/main.nf.test

diff --git a/nf-test.config b/nf-test.config
index 05d6fda..82d2611 100644
--- a/nf-test.config
+++ b/nf-test.config
@@ -1,5 +1,5 @@
 config {
-     // Location of nf-tests
+    // Location of nf-tests
     testsDir "."
 
     // nf-test directory used to create temporary files for each test
diff --git a/tests/handle_data.nf.test b/tests/handle_data.nf.test
new file mode 100644
index 0000000..0eddef6
--- /dev/null
+++ b/tests/handle_data.nf.test
@@ -0,0 +1,29 @@
+
+nextflow_workflow {
+
+    name "Test Workflow HANDLE_DATA"
+    script "../workflows/handle_data.nf"
+    workflow "HANDLE_DATA"
+
+    test("Test reproducibility of data handling") {
+
+        when {
+            workflow {
+                """
+                input[0] = Channel.fromPath(params.csv)
+                input[1] = Channel.fromPath(params.exp_conf)
+                input[2] = Channel.of("TESTING")
+                """
+            }
+        }
+
+        then {
+
+            assert workflow.success
+
+            with(workflow.out.data) {
+                assert size() == 2
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/tests/main.nf.test b/tests/main.nf.test
deleted file mode 100644
index f2451bf..0000000
--- a/tests/main.nf.test
+++ /dev/null
@@ -1,28 +0,0 @@
-nextflow_pipeline {
-
-    name "Test Workflow main.nf"
-    script "main.nf"
-    tag "PIPELINE"
-
-    test("Default test for reproducibility") {
-
-        when {
-            params {
-                outdir = "$outputDir"
-                // skip the check module step for now maybe change it in the future
-                check_model = false
-            }
-        }
-
-        then {
-            assertAll(
-                { assert workflow.success },
-                { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")).match("software_versions") },
-                { assert snapshot(
-                        path( "${params.outdir}/${workflow.runName}_" + "${workflow.start}/".replaceAll('[-:]', '_').split('\\.')[0] + "/test_with_split-shuffle/experiment_config.json" )
-                    ).match("output_files")
-                }
-            )
-        }
-    }
-}