diff --git a/subworkflows/nf-core/bcl_demultiplex/main.nf b/subworkflows/nf-core/bcl_demultiplex/main.nf
index 774c0362..f593c35e 100644
--- a/subworkflows/nf-core/bcl_demultiplex/main.nf
+++ b/subworkflows/nf-core/bcl_demultiplex/main.nf
@@ -76,11 +76,12 @@ workflow BCL_DEMULTIPLEX {
         ch_invalid_fastqs.view { "Invalid FASTQ file: $it" }
         println("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
 
-        // ch_invalid_fastqs
-        //     .ifEmpty { "No invalid FASTQ files found." }
-        //     .map { it -> it.toString() }
-        //     .collectFile(name: 'invalid_fastqs.txt', newLine: true)
-        //     .view()
+        // Collect and publish invalid FASTQ file paths
+        ch_invalid_fastqs
+            .ifEmpty { "No invalid FASTQ files found." }
+            .map { it -> it.toString() }
+            .collectFile(name: 'invalid_fastqs.txt', newLine: true)
+            .view()
 
     emit:
         fastq    = ch_fastq_with_meta
@@ -103,7 +104,7 @@ def generate_fastq_meta(ch_reads) {
         // Get readgroup; skip file if null (invalid FASTQ)
         def readgroup = readgroup_from_fastq(fastq)
         if (!readgroup) {
-            println("Warning 02 - Missing Header, FASTQ skipped: ${fastq}")
+            println("Warning 01 - Missing Header, FASTQ skipped: ${fastq}")
             ch_invalid_fastqs << "${fastq}"
             return []  // Return empty to exclude this file
         }
@@ -120,7 +121,8 @@ def generate_fastq_meta(ch_reads) {
 
         // Return metadata and fastq path
         return [meta, fastq]
-    }
+    }.filter { it[0] != null } // Filter out invalid fastq entries
+
     // Group by meta.id for paired-end (PE) samples
     .groupTuple(by: [0])
     // Add single_end flag based on fastq count
@@ -144,7 +146,7 @@ def readgroup_from_fastq(path) {
         }
 
         if (line == null || !line.startsWith('@')) {
-            println("Warning 01 - Skipping file: ${path}.\n" +
+            println("Warning 02 - Skipping file: ${path}.\n" +
                     "Expected a FASTQ file starting with '@', but found null.\n" +
                     "File is likely empty, corrupt or inaccessible.\n" +
                     "It will be skipped from further analyses.")
@@ -181,12 +183,10 @@ def readgroup_from_fastq(path) {
     }
 }
 
-// Collect and publish invalid FASTQ file paths
+// println("Current directory inside the process is: ${task.workDir}")
 process WriteInvalidFastqs {
     input:
     val ch_invalid_fastqs from ch_invalid_fastqs.collect()
-    // DEBUG
-    println("Current directory inside the process is: ${task.workDir}")
 
     script:
     """