fix the collision between input and output filename for single read

modules/nf-core/deacon/filter/main.nf

@@ -22,6 +22,7 @@ process DEACON_FILTER {
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
     def read_type = (reads instanceof List) ? "-o ${prefix}_1.fq -O ${prefix}_2.fq" : "> ${prefix}.fq" // deacon's automatic compression does not work
+    if (!(reads instanceof List) && reads.name == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
     deacon \\
         filter \\

modules/nf-core/deacon/filter/tests/main.nf.test

@@ -47,7 +47,13 @@ nextflow_process {
                     file(process.out.log[0][1]).name,
                     process.out.fastq_filtered,
                     process.out.findAll { key, val -> key.startsWith("versions") }
-                ).match()}
+                ).match()},
+                // Verify filtering actually occurred
+                {
+                    def log = new org.yaml.snakeyaml.Yaml().load(file(process.out.log[0][1]).text)
+                    assert log.seqs_in > 0 : "No reads were processed"
+                    assert log.seqs_out < log.seqs_in : "No reads were filtered out"
+                }
             )
         }
 

modules/nf-core/deacon/filter/tests/main.nf.test.snap

@@ -63,11 +63,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-05-08T18:41:01.264123579",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-02-12T12:46:45.282375511"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "sarscov2 - fastq - paired-end": {
         "content": [
@@ -94,11 +94,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-02-12T12:46:37.539497096",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-02-12T12:46:37.539497096"
+        }
     },
     "sarscov2 - fastq - single-end": {
         "content": [
@@ -122,10 +122,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-05-08T18:40:47.77635866",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-02-12T12:46:29.822244006"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }

subworkflows/nf-core/fastq_index_filter_deacon/tests/main.nf.test.snap

@@ -58,11 +58,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-05-08T18:43:04.833973809",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-02-13T09:19:12.052209052"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "sarscov2 - fastq - paired-end": {
         "content": [
@@ -89,11 +89,11 @@
             ],
             "test.json"
         ],
+        "timestamp": "2026-02-13T09:19:03.559444963",
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-02-13T09:19:03.559444963"
+        }
     },
     "sarscov2 - fastq - single-end": {
         "content": [
@@ -117,10 +117,10 @@
             ],
             "test.json"
         ],
+        "timestamp": "2026-05-08T18:42:51.063826149",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-02-13T09:18:55.835377502"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }