From 4bb0af18372f2009df260f53371d4c007de41aae Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 21 Jan 2025 18:20:35 +0000
Subject: [PATCH] Add test for no fasta

---
 tests/nofasta.nf.test | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 tests/nofasta.nf.test

diff --git a/tests/nofasta.nf.test b/tests/nofasta.nf.test
new file mode 100644
index 000000000..4413d4c41
--- /dev/null
+++ b/tests/nofasta.nf.test
@@ -0,0 +1,39 @@
+nextflow_pipeline {
+
+    name "Test pipeline by skipping trimming options"
+    script "../main.nf"
+
+    test("Params: no fasta") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+                skip_alignment = true
+                fasta = null
+                additional_fasta = null
+                salmon_index = null
+                transcript_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/d1f59361a013a8820c824d606f5853db0d6c7999/reference/transcriptome_match_gtf.fa"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
+}