From ab4d0571d5da8f663ef5c040899d3372d9467840 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Mon, 19 Feb 2024 16:14:55 -0600
Subject: [PATCH] test(gxf2bed): Add basic tests

---
 modules/nf-core/gxf2bed/main.nf            |  6 +--
 modules/nf-core/gxf2bed/tests/main.nf.test | 43 ++++++++++------------
 2 files changed, 23 insertions(+), 26 deletions(-)

diff --git a/modules/nf-core/gxf2bed/main.nf b/modules/nf-core/gxf2bed/main.nf
index efaa539f30e..cabd4613ece 100644
--- a/modules/nf-core/gxf2bed/main.nf
+++ b/modules/nf-core/gxf2bed/main.nf
@@ -1,5 +1,5 @@
 process GXF2BED {
-    tag '$bam'
+    tag '$gxf.baseName'
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
@@ -18,7 +18,7 @@ process GXF2BED {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${gxf.baseName}"
     """
     gxf2bed \\
         --input $gxf \\
@@ -32,7 +32,7 @@ process GXF2BED {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${gxf.baseName}"
     """
     touch ${prefix}.bed
 
diff --git a/modules/nf-core/gxf2bed/tests/main.nf.test b/modules/nf-core/gxf2bed/tests/main.nf.test
index 6702d4766c7..41cc57ec027 100644
--- a/modules/nf-core/gxf2bed/tests/main.nf.test
+++ b/modules/nf-core/gxf2bed/tests/main.nf.test
@@ -1,5 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test gxf2bed
 nextflow_process {
 
     name "Test Process GXF2BED"
@@ -10,20 +8,11 @@ nextflow_process {
     tag "modules_nfcore"
     tag "gxf2bed"
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
-    test("sarscov2 - bam") {
-
-        // TODO nf-core: If you are created a test for a chained module
-        // (the module requires running more than one process to generate the required output)
-        // add the 'setup' method here.
-        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
-
+    test("sarscov2 - gtf") {
         when {
             process {
                 """
-                // TODO nf-core: define inputs of the process here. Example:
-                
-                input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                input[0] = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
                 """
             }
         }
@@ -32,24 +21,18 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
-                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
             )
         }
-
     }
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
-    test("sarscov2 - bam - stub") {
+    test("sarscov2 - gtf - stub") {
 
         options "-stub"
 
         when {
             process {
                 """
-                // TODO nf-core: define inputs of the process here. Example:
-                
-                input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                input[0] = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
                 """
             }
         }
@@ -58,10 +41,24 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
             )
         }
-
     }
 
+    test("sarscov2 - gff") {
+        when {
+            process {
+                """
+                input[0] = file(params.test_data['homo_sapiens']['genome']['genome_gff3'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }