From 3128c7216fc6b79cc45a8f90d839d731e3ae7e5e Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 14 Oct 2024 14:20:04 +0200
Subject: [PATCH] Add working nf-test for the subworkflow

---
 .../tests/main.nf.test                        | 25 ++++++-------------
 .../tests/main.nf.test.snap                   |  6 ++---
 2 files changed, 10 insertions(+), 21 deletions(-)

diff --git a/subworkflows/local/generate_downstream_samplesheets/tests/main.nf.test b/subworkflows/local/generate_downstream_samplesheets/tests/main.nf.test
index 5363926..d1bcfed 100644
--- a/subworkflows/local/generate_downstream_samplesheets/tests/main.nf.test
+++ b/subworkflows/local/generate_downstream_samplesheets/tests/main.nf.test
@@ -8,36 +8,25 @@ nextflow_workflow {
     tag "subworkflows_local"
     tag "subworkflows/generate_downstream_samplesheets"
 
-    test("databases - taxprofiler") {
+    test("generate_downstream_samplesheets - taxprofiler") {
 
         when {
             params {
-                outdir                          = "$outputDir"
+                modules_testdata_base_path      = "https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/"
+                outdir                          = "."
                 generate_pipeline_samplesheets  = 'taxprofiler'
             }
             workflow {
                 """
                 input[0] = Channel.of(
                     [
-                        [id:'database', tool:'krakenuniq'],
-                        file('/workspace/createtaxdb/work/af/59cb1f95d809c3de6520bb0c0d0f6c/database')
-                    ],
-                    [
-                        [id:'database', tool:'centrifuge'],
-                        file('/workspace/createtaxdb/work/59/3a1df5c9f4b84a4ec3c8014aa13774/database')
+                        [id:'database', tool:'kraken2'],
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/genome/db/kraken2.tar.gz", checkIfExists: true)
                     ],
                     [
-                        [id:'database', tool:'kaiju'],
-                        file('/workspace/createtaxdb/work/87/865072d7fce3bbf8c5dfd867d16064/database.fmi')
-                    ],
-                    [
-                        [id:'database', tool:'diamond'],
-                        file('/workspace/createtaxdb/work/1b/f20ef16fbc0f4708db40d76410be5c/database.dmnd')
+                        [id:'database', tool:'krakenuniq'],
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/genome/db/krakenuniq.tar.gz", checkIfExists: true)
                     ],
-                    [
-                        [id:'database', tool:'malt'],
-                        file('/workspace/createtaxdb/work/4f/c630a9baab2c2f31f15fab1feec4f2/malt_index')
-                    ]
                 )
                 """
             }
diff --git a/subworkflows/local/generate_downstream_samplesheets/tests/main.nf.test.snap b/subworkflows/local/generate_downstream_samplesheets/tests/main.nf.test.snap
index ef7ea51..3116e6d 100644
--- a/subworkflows/local/generate_downstream_samplesheets/tests/main.nf.test.snap
+++ b/subworkflows/local/generate_downstream_samplesheets/tests/main.nf.test.snap
@@ -1,12 +1,12 @@
 {
-    "databases - taxprofiler": {
+    "generate_downstream_samplesheets - taxprofiler": {
         "content": [
-            "taxprofiler.csv:md5,dc4cb1c64d2d48273eb2125266b315bf"
+            "./downstream_samplesheets/taxprofiler.csv"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-10T22:10:48.802711152"
+        "timestamp": "2024-10-14T14:19:50.381431215"
     }
 }
\ No newline at end of file