diff --git a/workflow/nextflow.config b/workflow/nextflow.config
index 9405aabf9153e22a2c2613f97b806160a0da3436..3fe4140412a6004b64f69b54d0fc0a9bccaddfb3 100755
--- a/workflow/nextflow.config
+++ b/workflow/nextflow.config
@@ -1,107 +1,70 @@
 // CONFIGURATION FILE
 
-// Pipeline parameter default values, can be modified by user when calling pipeline on command line (e.g. --ont_reads_fq sample_1.fastq) ##
+// Pipeline parameter default values, can be modified by user when calling
+// pipeline on command line (e.g. --ont_reads_fq sample_1.fastq)
 
 // Input reference fasta file
 params.ref = 'None' 
-
 // Step of pipeline to execute
 params.step = 'None'
-
 // Output directory for pipeline results
 params.out_dir = "output_directory/" 
-
 // directory of basecalling data
 params.basecall_path = 'None' 
-
 // MAPQ filtering threshold for bam files, 0 for no filtering
 params.mapq = "10" 
-
 // Quality score threshold
 params.qscore_thresh = "9"
-
 // Desired basecall speed 
 params.basecall_speed = "hac"
-
 // Desired basecaller modifications
 params.basecall_mods = false
-
 // Threshold for mapped reasds
 params.min_mapped_reads_thresh = 500
-
 // Desired basecall configuration
 params.basecall_config = "None"
-
 // Type of read trimming during basecalling ("all", "primers", "adapters", "none")
 params.basecall_trim = "none"
-
 // Basecalling demultiplexing
 params.basecall_demux = false
-
 // CPU vs GPU basecalling
 params.basecall_compute = "gpu"
-
 // Trim barcodes (only counts if demultiplexing is enabled)
 params.trim_barcode = "True"
-
 // Add prefix to all output files
 params.prefix = "None"
-
 // Which GPU devices to use for basecalling?
 params.gpu_devices = "all"
-
 // Previous results
 params.steps_2_and_3_input_directory = "None"
-
 // MultiQC config
 params.multiqc_config = "None"
-
 // Are the files from MinKNOW barcoded or not 
 params.is_barcoded = true
 
-
-
-
+// Set queue size for the executor
 if (params.step == 1) {
-
 	queue_size = 1
-
 } else {
-
 	queue_size = 5
-
 }
-
 process { 
-
     // Define local cpu execution
-
     withLabel: cpu {
         executor='local'
     }
-    
     // Define local gpu execution
     withLabel: gpu {
-        
         executor='local'
         containerOptions = '--nv'
     }
-   
     // Define the singularity container for every process, will pull container from the cloud
     container = "library://joaochrusciel/nanopore/ont_methylation:2024-10-18"
-
 }
-
 executor {
-
 	name = 'local'
 	queueSize = queue_size
-
 }
-
-
 apptainer {
-
 	enabled = true
-
 }