diff --git a/sub_workflows/BASECALLING.nf b/sub_workflows/BASECALLING.nf
index cc07e68e13e26a8707b67716a609de5bda7c7c41..1e0a62fb33dd1c0474f5d3c909eeabc1e86790c5 100755
--- a/sub_workflows/BASECALLING.nf
+++ b/sub_workflows/BASECALLING.nf
@@ -2,42 +2,42 @@ include { FAST5_to_POD5 ; BASECALL_CPU ; BASECALL_CPU_DEMUX ; BASECALL_GPU ; BAS
 
 workflow BASECALLING {
     take:
-    pod5_path
-    fast5_path
-    speed
-    modifications
-    config
-    trim
-    quality_score
-    trim_barcode
-    devices
-    ref
+        pod5_path
+        fast5_path
+        speed
+        modifications
+        config
+        trim
+        quality_score
+        trim_barcode
+        devices
+        ref
+    
     main:
-
-    FAST5_to_POD5(fast5_path)
-    pod5_path = FAST5_to_POD5.out.mix(pod5_path)
-    if (params.basecall_compute?.equalsIgnoreCase("cpu")) {
-        if (params.basecall_demux == true) {
-            BASECALL_CPU_DEMUX(pod5_path, speed, modifications, config, trim, quality_score, trim_barcode, devices, ref)
-            bams = BASECALL_CPU_DEMUX.out.bam.toSortedList { a, b -> a[0] <=> b[0] }.flatten().buffer(size: 2)
-            txts = BASECALL_CPU_DEMUX.out.txt.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten()
-        }
-        else {
-            BASECALL_CPU(pod5_path, speed, modifications, config, trim, quality_score, devices, ref)
-            bams = BASECALL_CPU.out.bam.toSortedList { a, b -> a[0] <=> b[0] }.flatten().buffer(size: 2)
-            txts = BASECALL_CPU.out.txt.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten()
-        }
-    }
-    else if (params.basecall_compute?.equalsIgnoreCase("gpu")) {
-        if (params.basecall_demux == true) {
-            BASECALL_GPU_DEMUX(pod5_path, speed, modifications, config, trim, quality_score, trim_barcode, devices, ref)
-            bams = BASECALL_GPU_DEMUX.out.bam.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten()
-            txts = BASECALL_GPU_DEMUX.out.txt.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten()
+        FAST5_to_POD5(fast5_path)
+        pod5_path = FAST5_to_POD5.out.mix(pod5_path)
+        if (params.basecall_compute?.equalsIgnoreCase("cpu")) {
+            if (params.basecall_demux == true) {
+                BASECALL_CPU_DEMUX(pod5_path, speed, modifications, config, trim, quality_score, trim_barcode, devices, ref)
+                bams = BASECALL_CPU_DEMUX.out.bam.toSortedList { a, b -> a[0] <=> b[0] }.flatten().buffer(size: 2)
+                txts = BASECALL_CPU_DEMUX.out.txt.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten()
+            }
+            else {
+                BASECALL_CPU(pod5_path, speed, modifications, config, trim, quality_score, devices, ref)
+                bams = BASECALL_CPU.out.bam.toSortedList { a, b -> a[0] <=> b[0] }.flatten().buffer(size: 2)
+                txts = BASECALL_CPU.out.txt.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten()
+            }
         }
-        else {
-            BASECALL_GPU(pod5_path, speed, modifications, config, trim, quality_score, devices, ref)
-            bams = BASECALL_GPU.out.bam.toSortedList { a, b -> a[0] <=> b[0] }.flatten().buffer(size: 2)
-            txts = BASECALL_GPU.out.txt.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten()
+        else if (params.basecall_compute?.equalsIgnoreCase("gpu")) {
+            if (params.basecall_demux == true) {
+                BASECALL_GPU_DEMUX(pod5_path, speed, modifications, config, trim, quality_score, trim_barcode, devices, ref)
+                bams = BASECALL_GPU_DEMUX.out.bam.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten()
+                txts = BASECALL_GPU_DEMUX.out.txt.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten()
+            }
+            else {
+                BASECALL_GPU(pod5_path, speed, modifications, config, trim, quality_score, devices, ref)
+                bams = BASECALL_GPU.out.bam.toSortedList { a, b -> a[0] <=> b[0] }.flatten().buffer(size: 2)
+                txts = BASECALL_GPU.out.txt.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten()
+            }
         }
-    }
 }
diff --git a/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf b/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf
index 2a007cc8f20cc69823153ffd84761e4e08f12f8e..90dc60c6d9260db7d5b5d7666177d211a0067493 100755
--- a/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf
+++ b/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf
@@ -6,51 +6,51 @@ include { CONVERT_INPUT_FROM_MINKNOW_BARCODED ; CONVERT_INPUT_FROM_MINKNOW_NOT_B
 
 workflow FILTERING_AND_QC_FROM_MINKNOW {
     take:
-    input
-    mapq
-    quality_score
+        input
+        mapq
+        quality_score
+
     main:
-    if (params.is_barcoded == true) {
-        CONVERT_INPUT_FROM_MINKNOW_BARCODED(input)
-        converted_input = CONVERT_INPUT_FROM_MINKNOW_BARCODED.out
-    }
-    else if (params.is_barcoded == false) {
-        CONVERT_INPUT_FROM_MINKNOW_NOT_BARCODED(input)
-        converted_input = CONVERT_INPUT_FROM_MINKNOW_NOT_BARCODED.out
-    }
-    FILTER_BAM(
-        converted_input.bam.flatten().map { file -> tuple(file.baseName, file) }.toSortedList { a, b -> a[0] <=> b[0] }.flatten().buffer(size: 2),
-        converted_input.txt.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten(),
-        mapq,
-    )
-    PYCOQC_NO_FILTER(
-        FILTER_BAM.out.id,
-        FILTER_BAM.out.total_bam,
-        FILTER_BAM.out.total_bai,
-        FILTER_BAM.out.filtered_bam,
-        FILTER_BAM.out.filtered_bai,
-        FILTER_BAM.out.unfiltered_flagstat,
-        FILTER_BAM.out.filtered_flagstat,
-        FILTER_BAM.out.txt,
-        quality_score,
-    )
-    PYCOQC_FILTER(
-        PYCOQC_NO_FILTER.out.id,
-        PYCOQC_NO_FILTER.out.filtered_bam,
-        PYCOQC_NO_FILTER.out.filtered_bai,
-        PYCOQC_NO_FILTER.out.unfiltered_flagstat,
-        PYCOQC_NO_FILTER.out.filtered_flagstat,
-        PYCOQC_NO_FILTER.out.txt,
-        quality_score,
-        PYCOQC_NO_FILTER.out.unfiltered_pyco_json,
-    )
-    MAKE_QC_REPORT(
-        PYCOQC_FILTER.out.id,
-        PYCOQC_FILTER.out.unfiltered_flagstat,
-        PYCOQC_FILTER.out.filtered_flagstat,
-        PYCOQC_FILTER.out.unfiltered_pyco_json,
-        PYCOQC_FILTER.out.filtered_pyco_json,
-        mapq,
-        quality_score,
-    )
+        if (params.is_barcoded == true) {
+            CONVERT_INPUT_FROM_MINKNOW_BARCODED(input)
+            converted_input = CONVERT_INPUT_FROM_MINKNOW_BARCODED.out
+        } else if (params.is_barcoded == false) {
+            CONVERT_INPUT_FROM_MINKNOW_NOT_BARCODED(input)
+            converted_input = CONVERT_INPUT_FROM_MINKNOW_NOT_BARCODED.out
+        }
+        FILTER_BAM(
+            converted_input.bam.flatten().map { file -> tuple(file.baseName, file) }.toSortedList { a, b -> a[0] <=> b[0] }.flatten().buffer(size: 2),
+            converted_input.txt.toSortedList { a, b -> a.baseName <=> b.baseName }.flatten(),
+            mapq,
+        )
+        PYCOQC_NO_FILTER(
+            FILTER_BAM.out.id,
+            FILTER_BAM.out.total_bam,
+            FILTER_BAM.out.total_bai,
+            FILTER_BAM.out.filtered_bam,
+            FILTER_BAM.out.filtered_bai,
+            FILTER_BAM.out.unfiltered_flagstat,
+            FILTER_BAM.out.filtered_flagstat,
+            FILTER_BAM.out.txt,
+            quality_score,
+        )
+        PYCOQC_FILTER(
+            PYCOQC_NO_FILTER.out.id,
+            PYCOQC_NO_FILTER.out.filtered_bam,
+            PYCOQC_NO_FILTER.out.filtered_bai,
+            PYCOQC_NO_FILTER.out.unfiltered_flagstat,
+            PYCOQC_NO_FILTER.out.filtered_flagstat,
+            PYCOQC_NO_FILTER.out.txt,
+            quality_score,
+            PYCOQC_NO_FILTER.out.unfiltered_pyco_json,
+        )
+        MAKE_QC_REPORT(
+            PYCOQC_FILTER.out.id,
+            PYCOQC_FILTER.out.unfiltered_flagstat,
+            PYCOQC_FILTER.out.filtered_flagstat,
+            PYCOQC_FILTER.out.unfiltered_pyco_json,
+            PYCOQC_FILTER.out.filtered_pyco_json,
+            mapq,
+            quality_score,
+        )
 }
diff --git a/sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf b/sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf
index bf14a514113cce3d74cbcf2585a42b7dda397e4f..6f3a7113be41b75386ae141a2aab654777e74532 100755
--- a/sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf
+++ b/sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf
@@ -3,43 +3,44 @@
 include { PYCOQC_NO_FILTER ; PYCOQC_FILTER } from '../modules/pycoqc.nf'
 include { FILTER_BAM } from '../modules/filter_bam.nf'
 include { MAKE_QC_REPORT } from '../modules/num_reads_report.nf'
+
 workflow FILTERING_AND_QC_FROM_STEP_1 {
     take:
-    bams
-    txts
-    mapq
-    quality_score
+        bams
+        txts
+        mapq
+        quality_score
 
     main:
-    FILTER_BAM(bams, txts, mapq)
-    PYCOQC_NO_FILTER(
-        FILTER_BAM.out.id,
-        FILTER_BAM.out.total_bam,
-        FILTER_BAM.out.total_bai,
-        FILTER_BAM.out.filtered_bam,
-        FILTER_BAM.out.filtered_bai,
-        FILTER_BAM.out.unfiltered_flagstat,
-        FILTER_BAM.out.filtered_flagstat,
-        FILTER_BAM.out.txt,
-        quality_score,
-    )
-    PYCOQC_FILTER(
-        PYCOQC_NO_FILTER.out.id,
-        PYCOQC_NO_FILTER.out.filtered_bam,
-        PYCOQC_NO_FILTER.out.filtered_bai,
-        PYCOQC_NO_FILTER.out.unfiltered_flagstat,
-        PYCOQC_NO_FILTER.out.filtered_flagstat,
-        PYCOQC_NO_FILTER.out.txt,
-        quality_score,
-        PYCOQC_NO_FILTER.out.unfiltered_pyco_json,
-    )
-    MAKE_QC_REPORT(
-        PYCOQC_FILTER.out.id,
-        PYCOQC_FILTER.out.unfiltered_flagstat,
-        PYCOQC_FILTER.out.filtered_flagstat,
-        PYCOQC_FILTER.out.unfiltered_pyco_json,
-        PYCOQC_FILTER.out.filtered_pyco_json,
-        mapq,
-        quality_score,
-    )
+        FILTER_BAM(bams, txts, mapq)
+        PYCOQC_NO_FILTER(
+            FILTER_BAM.out.id,
+            FILTER_BAM.out.total_bam,
+            FILTER_BAM.out.total_bai,
+            FILTER_BAM.out.filtered_bam,
+            FILTER_BAM.out.filtered_bai,
+            FILTER_BAM.out.unfiltered_flagstat,
+            FILTER_BAM.out.filtered_flagstat,
+            FILTER_BAM.out.txt,
+            quality_score,
+        )
+        PYCOQC_FILTER(
+            PYCOQC_NO_FILTER.out.id,
+            PYCOQC_NO_FILTER.out.filtered_bam,
+            PYCOQC_NO_FILTER.out.filtered_bai,
+            PYCOQC_NO_FILTER.out.unfiltered_flagstat,
+            PYCOQC_NO_FILTER.out.filtered_flagstat,
+            PYCOQC_NO_FILTER.out.txt,
+            quality_score,
+            PYCOQC_NO_FILTER.out.unfiltered_pyco_json,
+        )
+        MAKE_QC_REPORT(
+            PYCOQC_FILTER.out.id,
+            PYCOQC_FILTER.out.unfiltered_flagstat,
+            PYCOQC_FILTER.out.filtered_flagstat,
+            PYCOQC_FILTER.out.unfiltered_pyco_json,
+            PYCOQC_FILTER.out.filtered_pyco_json,
+            mapq,
+            quality_score,
+        )
 }
diff --git a/sub_workflows/MODKIT_AND_MULTIQC.nf b/sub_workflows/MODKIT_AND_MULTIQC.nf
index 346e2dd008915efc23652e84603e291e1f25de07..35294c78f20ee2aef614636017fef98b5f09af10 100755
--- a/sub_workflows/MODKIT_AND_MULTIQC.nf
+++ b/sub_workflows/MODKIT_AND_MULTIQC.nf
@@ -1,5 +1,4 @@
 // Import Modules
-
 include { MULTIQC } from '../modules/multiqc.nf'
 include { MODKIT } from '../modules/modkit.nf'
 include { MERGE_QC_REPORT } from '../modules//num_reads_report.nf'