Merge branch 'master' into master

nf-core · Feb 26, 2025 · fbd727e · fbd727e
2 parents cdd3ddb + 804110b
commit fbd727e
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Showing 37 changed files with 1,985 additions and 849 deletions.
diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf
@@ -18,7 +18,6 @@ process CAT_FASTQ {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()]
     if (meta.single_end) {
@@ -31,6 +30,8 @@ process CAT_FASTQ {
                 cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
             END_VERSIONS
             """
+        } else {
+            error("Could not find any FASTQ files to concatenate in the process input")
         }
     }
     else {
@@ -47,6 +48,8 @@ process CAT_FASTQ {
                 cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
             END_VERSIONS
             """
+        } else {
+            error("Could not find any FASTQ file pairs to concatenate in the process input")
         }
     }
 
@@ -63,6 +66,8 @@ process CAT_FASTQ {
                 cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
             END_VERSIONS
             """
+        } else {
+            error("Could not find any FASTQ files to concatenate in the process input")
         }
     }
     else {
@@ -76,6 +81,8 @@ process CAT_FASTQ {
                 cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
             END_VERSIONS
             """
+        } else {
+            error("Could not find any FASTQ file pairs to concatenate in the process input")
         }
     }
 }
diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test
@@ -243,4 +243,92 @@ nextflow_process {
             )
         }
     }
+
+    test("test_cat_fastq_single_end_no_files") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    []
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_paired_end_no_files") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    []
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_single_end_no_files - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ], // meta map
+                    []
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() }
+            )
+        }
+    }
+
+    test("test_cat_fastq_paired_end_no_files - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:false ], // meta map
+                    []
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert snapshot(process.stdout.find { it.contains("-- Check script") }.split(" -- Check script")[0]).match() }
+            )
+        }
+    }
 }