From 01b1e4b0f6c27ea8b5c2c7f4397f22afb6f30309 Mon Sep 17 00:00:00 2001
From: kylacochrane <Kyla.Cochrane@phac-aspc.gc.ca>
Date: Mon, 17 Jun 2024 16:32:10 -0400
Subject: [PATCH] Added tests with pd_columns

---
 .../columns/keep-zero-loci-empty-file.txt     |  1 +
 tests/pipelines/main_missing_alleles.nf.test  | 36 +++++++++++++++++++
 2 files changed, 37 insertions(+)
 create mode 100644 tests/data/columns/keep-zero-loci-empty-file.txt

diff --git a/tests/data/columns/keep-zero-loci-empty-file.txt b/tests/data/columns/keep-zero-loci-empty-file.txt
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/tests/data/columns/keep-zero-loci-empty-file.txt
@@ -0,0 +1 @@
+
diff --git a/tests/pipelines/main_missing_alleles.nf.test b/tests/pipelines/main_missing_alleles.nf.test
index 7d24c06..51b2e71 100644
--- a/tests/pipelines/main_missing_alleles.nf.test
+++ b/tests/pipelines/main_missing_alleles.nf.test
@@ -134,5 +134,41 @@ nextflow_pipeline {
             assert iridanext_metadata.sampleQ."address" == "1"
         }
     }
+
+    test("Test fail pipeline if non-existent columns file is passed") {
+        tag "pipeline_failure_columns_no_exist"
+
+        when {
+            params {
+                input = "$baseDir/tests/data/samplesheets/samplesheet-hash_missing.csv"
+                outdir = "results"
+
+                pd_columns = "./no-exist"
+            }
+        }
+
+        then {
+            assert workflow.failed
+            assert workflow.stderr.contains("* --pd_columns: the file or directory './no-exist' does not exist.")
+        }
+    }
+
+    test("Test failure of pipeline when keeping no loci") {
+        tag "pipeline_keep_zero_loci"
+
+        when {
+            params {
+                input = "$baseDir/tests/data/samplesheets/samplesheet-hash_missing.csv"
+                outdir = "results"
+
+                gm_thresholds = "0"
+                pd_columns = "$baseDir/tests/data/columns/keep-zero-loci-empty-file.txt"
+            }
+        }
+
+        then {
+            assert workflow.failed
+        }
+    }
 }