diff --git a/conf/modules.config b/conf/modules.config
index 6b85e19..620ce14 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -26,35 +26,7 @@ process {
         ]
     }
 
-withName: CUTADAPT {
-    ext.args = { [
-        "--minimum-length 1",
-        "-O ${params.cutadapt_min_overlap}",
-        "-e ${params.cutadapt_max_error_rate}",
-        // Use primers from the samplesheet if available, otherwise fall back to params
-        meta.fw_primer ? "-g ${meta.fw_primer}" : (params.FW_primer ? "-g ${params.FW_primer}" : ''),
-        meta.rv_primer ? "-G ${meta.rv_primer}" : (params.RV_primer ? "-G ${params.RV_primer}" : ''),
-        params.retain_untrimmed ? '' : "--discard-untrimmed"
-    ].findAll { it }.join(' ').trim() } // Remove empty strings and join arguments
-
-    ext.prefix = { "${meta.id}.trimmed" }
-
-    publishDir = [
-        [   path: { "${params.outdir}/cutadapt" },
-            mode: params.publish_dir_mode,
-            pattern: "*.log"
-        ],
-        [   path: { "${params.outdir}/cutadapt/trimmed_reads" },
-            mode: params.publish_dir_mode,
-            pattern: "*.trim.fastq.gz",
-            enabled: params.save_intermediates
-        ]
-    ]
-}
-
-
 
-//
     withName: MERGE_BARCODES_SAMPLESHEET {
         publishDir = [
             path: { "${params.outdir}/fastq_pass_merged" },
@@ -120,6 +92,32 @@ withName: CUTADAPT {
     }
 
 
+    withName: CUTADAPT {
+        ext.args = { [
+        "--minimum-length 1",
+        "-O ${params.cutadapt_min_overlap}",
+        "-e ${params.cutadapt_max_error_rate}",
+        // Use primers from the samplesheet if available, otherwise fall back to params
+        meta.fw_primer ? "-g ${meta.fw_primer}" : (params.FW_primer ? "-g ${params.FW_primer}" : ''),
+        meta.rv_primer ? "-G ${meta.rv_primer}" : (params.RV_primer ? "-G ${params.RV_primer}" : ''),
+        params.retain_untrimmed ? '' : "--discard-untrimmed"
+        ].findAll { it }.join(' ').trim() } // Remove empty strings and join arguments
+
+        ext.prefix = { "${meta.id}.trimmed" }
+
+        publishDir = [
+        [   path: { "${params.outdir}/cutadapt" },
+            mode: params.publish_dir_mode,
+            pattern: "*.log"
+        ],
+        [   path: { "${params.outdir}/cutadapt/trimmed_reads" },
+            mode: params.publish_dir_mode,
+            pattern: "*.trim.fastq.gz",
+            enabled: params.save_intermediates
+        ]
+     ]
+   }
+
 
 
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
@@ -204,8 +202,7 @@ withName: CUTADAPT {
             ]
         ]
     }
-
+ 
 
 
 }
-
diff --git a/workflows/gmsemu.nf b/workflows/gmsemu.nf
index 902da04..d9b3e49 100644
--- a/workflows/gmsemu.nf
+++ b/workflows/gmsemu.nf
@@ -99,30 +99,47 @@ workflow GMSEMU {
     )
     ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
-
-
-    // Processing based on seqtype
     if (params.seqtype == "map-ont") {
-        // Long-read processing
         NANOPLOT1(INPUT_CHECK.out.reads)
         ch_versions = ch_versions.mix(NANOPLOT1.out.versions.first())
 
-	  //  NANOPLOT2 (
-	  //      INPUT_CHECK.out.reads
-	  //  )
+        if (params.adapter_trimming && !params.quality_filtering) {
+            PORECHOP_ABI(INPUT_CHECK.out.reads)
+
+            ch_processed_reads = PORECHOP_ABI.out.reads
+                .map { meta, reads -> [meta + [single_end: 1], reads] }
+
+            ch_versions = ch_versions.mix(PORECHOP_ABI.out.versions.first())
+            ch_multiqc_files = ch_multiqc_files.mix(PORECHOP_ABI.out.log)
+
+        } else if (!params.adapter_trimming && params.quality_filtering) { 
+            ch_processed_reads = FILTLONG(
+                INPUT_CHECK.out.reads.map { meta, reads -> [meta, [], reads] }
+            ).reads
 
-        if (params.adapter_trimming  && !params.quality_filtering  ) {
+            ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
+            ch_multiqc_files = ch_multiqc_files.mix(FILTLONG.out.log)
+
+        } else if (params.adapter_trimming && params.quality_filtering) {
+            // Both adapter trimming and quality filtering
             PORECHOP_ABI(INPUT_CHECK.out.reads)
-            ch_clipped_reads = PORECHOP_ABI.out.reads.map { meta, reads -> [meta + [single_end: 1], reads] }
-            ch_processed_reads = FILTLONG(ch_clipped_reads.map { meta, reads -> [meta, [], reads] }).reads
+
+            ch_clipped_reads = PORECHOP_ABI.out.reads
+                .map { meta, reads -> [meta + [single_end: 1], reads] }
+
+            ch_processed_reads = FILTLONG(
+                ch_clipped_reads.map { meta, reads -> [meta, [], reads] }
+            ).reads
 
             ch_versions = ch_versions.mix(PORECHOP_ABI.out.versions.first())
             ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
+            ch_multiqc_files = ch_multiqc_files.mix(PORECHOP_ABI.out.log)
+            ch_multiqc_files = ch_multiqc_files.mix(FILTLONG.out.log)
+
         } else {
             ch_processed_reads = INPUT_CHECK.out.reads
         }
 
-
     } else if (params.seqtype == "sr") {
         // Short-read processing
         if (!params.skip_cutadapt) {
@@ -137,6 +154,7 @@ workflow GMSEMU {
     }
 
 
+
     // Run EMU_ABUNDANCE
     EMU_ABUNDANCE(ch_processed_reads)
     ch_versions = ch_versions.mix(EMU_ABUNDANCE.out.versions.first())