Fix random seed by default and change test data

Use small cov2 readset for testing, set genome size very low to allow subsampling

Author: dwells-eit

modules/nf-core/autocycler/subsample/main.nf

@@ -22,6 +22,8 @@ process AUTOCYCLER_SUBSAMPLE {
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
+    // fix random seed for reproducibility if not specified in command line
+    if (!(args ==~ /.*--seed.*/)) {args += " --seed 42"}
     """
     autocycler subsample \\
         $args \\

modules/nf-core/autocycler/subsample/tests/main.nf.test

@@ -3,7 +3,6 @@ nextflow_process {
     name "Test Process AUTOCYCLER_SUBSAMPLE"
     script "../main.nf"
     process "AUTOCYCLER_SUBSAMPLE"
-    config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
@@ -13,16 +12,13 @@ nextflow_process {
     test("Pseudomonas_fluorescens - fastq_gz") {
 
         when {
-            params{
-                module_args = '--seed 1234'
-            }
             process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file('https://github.com/nf-core/test-datasets/raw/refs/heads/bacass/nanopore/subset15000.fq.gz', checkIfExists: true), // reads
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test.fastq.gz', checkIfExists: true), // reads
                 ]
-                input[1] = 30000 // genome size
+                input[1] = 300 // set genome size very small to get sufficient depth
                 """
             }
         }
@@ -41,9 +37,6 @@ nextflow_process {
         options "-stub"
 
         when {
-            params{
-                module_args = ''
-            }
             process {
                 """
                 input[0] = [
@@ -58,6 +51,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
+                { assert snapshot(process.out).match() }
             )
         }
 

modules/nf-core/autocycler/subsample/tests/main.nf.test.snap

@@ -9,10 +9,10 @@
                             "single_end": false
                         },
                         [
-                            "sample_01.fastq.gz:md5,b1cc8c9ee163474d67d7889e25e4e0ae",
-                            "sample_02.fastq.gz:md5,c3124b6b062158d41e822a9ff16df988",
-                            "sample_03.fastq.gz:md5,3f2db5a32a4a0cfdbb5a58b5a81f3a92",
-                            "sample_04.fastq.gz:md5,28c99f7e4565924229a980500c185802"
+                            "sample_01.fastq.gz:md5,7a9ac52d5071893300808fc11091bdbb",
+                            "sample_02.fastq.gz:md5,e1e73dc1f31aa8b30834286d13ab500a",
+                            "sample_03.fastq.gz:md5,e5cead9b5bbdf541062423065a5b6f51",
+                            "sample_04.fastq.gz:md5,312cb2589411da99ecfd50392e999cdc"
                         ]
                     ]
                 ],
@@ -26,10 +26,10 @@
                             "single_end": false
                         },
                         [
-                            "sample_01.fastq.gz:md5,b1cc8c9ee163474d67d7889e25e4e0ae",
-                            "sample_02.fastq.gz:md5,c3124b6b062158d41e822a9ff16df988",
-                            "sample_03.fastq.gz:md5,3f2db5a32a4a0cfdbb5a58b5a81f3a92",
-                            "sample_04.fastq.gz:md5,28c99f7e4565924229a980500c185802"
+                            "sample_01.fastq.gz:md5,7a9ac52d5071893300808fc11091bdbb",
+                            "sample_02.fastq.gz:md5,e1e73dc1f31aa8b30834286d13ab500a",
+                            "sample_03.fastq.gz:md5,e5cead9b5bbdf541062423065a5b6f51",
+                            "sample_04.fastq.gz:md5,312cb2589411da99ecfd50392e999cdc"
                         ]
                     ]
                 ],
@@ -42,6 +42,41 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.4"
         },
-        "timestamp": "2025-10-27T17:18:38.77396493"
+        "timestamp": "2025-10-29T08:36:17.505206711"
+    },
+    "Pseudomonas_fluorescens - fastq_gz - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "sample_00.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,0abfe90f7bd1d54716b236993073b514"
+                ],
+                "subsampled_reads": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "sample_00.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0abfe90f7bd1d54716b236993073b514"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.4"
+        },
+        "timestamp": "2025-10-29T08:07:36.406154106"
     }
 }