diff --git a/README.md b/README.md
index e62a135e9f011d52512839b699c863c780eca26a..ee239bc89d5fb674d3abf3ea3fbdc01bd406f096 100755
--- a/README.md
+++ b/README.md
@@ -254,7 +254,7 @@ The following examples assume your current directory is the root directory of th
 1. STEP 1: GPU basecalling without demultiplexing
 
     ```sh
-    nextflow ./workflow/main.nf \
+    nextflow ./src/main.nf \
             --basecall_path "$BASECALL_PATH" \
             --basecall_speed "hac" \
             --step 1 \
@@ -274,7 +274,7 @@ The following examples assume your current directory is the root directory of th
 1. STEP 2A: Alignment Filtering and Quality Control from STEP 1
 
     ```sh
-    nextflow ./workflow/main.nf \
+    nextflow ./src/main.nf \
               --steps_2_and_3_input_directory "./results/$OUTPUT_DIR_NAME/" \
               --min_mapped_reads_thresh 500 \
               --qscore_thresh 9 \
@@ -286,7 +286,7 @@ The following examples assume your current directory is the root directory of th
 1. STEP 2B (MinKNOW): Alignment Filtering and Quality Control from MinKNOW basecalling and alignment (bam files were generated by MinKNOW)
 
     ```sh
-    nextflow ./workflow/main.nf \
+    nextflow ./src/main.nf \
               --steps_2_and_3_input_directory "./results/$OUTPUT_DIR_NAME/" \
               --min_mapped_reads_thresh 500 \
               --is_barcoded "True" \
@@ -299,7 +299,7 @@ The following examples assume your current directory is the root directory of th
 1. STEP 3: Methylation calling and MultiQC report
 
     ```sh
-    nextflow ./workflow/main.nf \
+    nextflow ./src/main.nf \
               --steps_2_and_3_input_directory "./results/$OUTPUT_DIR_NAME/" \
               --multiqc_config "./references/multiqc_config.yaml" \
               --step 3 \
diff --git a/workflow/bin/merge_files.py b/src/bin/merge_files.py
similarity index 100%
rename from workflow/bin/merge_files.py
rename to src/bin/merge_files.py
diff --git a/workflow/main.nf b/src/main.nf
similarity index 95%
rename from workflow/main.nf
rename to src/main.nf
index 6b45ca519e429009579891ee0ac54220b26ab312..e0a983f8e20e276b1d5a7be9892be70fa1a83b45 100755
--- a/workflow/main.nf
+++ b/src/main.nf
@@ -46,10 +46,10 @@ MultiQC configuration file                          : ${params.multiqc_config}
 }
 
 // Import Workflows
-include {BASECALLING} from '../sub_workflows/BASECALLING'
-include {FILTERING_AND_QC_FROM_STEP_1} from '../sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf'
-include {FILTERING_AND_QC_FROM_MINKNOW} from '../sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf'
-include {MODKIT_AND_MULTIQC} from '../sub_workflows/MODKIT_AND_MULTIQC.nf'
+include {BASECALLING} from './sub_workflows/BASECALLING'
+include {FILTERING_AND_QC_FROM_STEP_1} from './sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf'
+include {FILTERING_AND_QC_FROM_MINKNOW} from './sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf'
+include {MODKIT_AND_MULTIQC} from './sub_workflows/MODKIT_AND_MULTIQC.nf'
 
 // Define initial files and channels
 if (params.step.toString() == "1") {
diff --git a/modules/basecall.nf b/src/modules/basecall.nf
similarity index 100%
rename from modules/basecall.nf
rename to src/modules/basecall.nf
diff --git a/modules/calculate_coverage.nf b/src/modules/calculate_coverage.nf
similarity index 100%
rename from modules/calculate_coverage.nf
rename to src/modules/calculate_coverage.nf
diff --git a/modules/convert_input_from_minknow.nf b/src/modules/convert_input_from_minknow.nf
similarity index 100%
rename from modules/convert_input_from_minknow.nf
rename to src/modules/convert_input_from_minknow.nf
diff --git a/modules/filter_bam.nf b/src/modules/filter_bam.nf
similarity index 100%
rename from modules/filter_bam.nf
rename to src/modules/filter_bam.nf
diff --git a/modules/modkit.nf b/src/modules/modkit.nf
similarity index 100%
rename from modules/modkit.nf
rename to src/modules/modkit.nf
diff --git a/modules/multiqc.nf b/src/modules/multiqc.nf
similarity index 100%
rename from modules/multiqc.nf
rename to src/modules/multiqc.nf
diff --git a/modules/num_reads_report.nf b/src/modules/num_reads_report.nf
similarity index 100%
rename from modules/num_reads_report.nf
rename to src/modules/num_reads_report.nf
diff --git a/modules/pycoqc.nf b/src/modules/pycoqc.nf
similarity index 100%
rename from modules/pycoqc.nf
rename to src/modules/pycoqc.nf
diff --git a/workflow/nextflow.config b/src/nextflow.config
similarity index 100%
rename from workflow/nextflow.config
rename to src/nextflow.config
diff --git a/sub_workflows/BASECALLING.nf b/src/sub_workflows/BASECALLING.nf
similarity index 100%
rename from sub_workflows/BASECALLING.nf
rename to src/sub_workflows/BASECALLING.nf
diff --git a/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf b/src/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf
similarity index 100%
rename from sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf
rename to src/sub_workflows/FILTERING_AND_QC_FROM_MINKNOW.nf
diff --git a/sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf b/src/sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf
similarity index 100%
rename from sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf
rename to src/sub_workflows/FILTERING_AND_QC_FROM_STEP_1.nf
diff --git a/sub_workflows/MODKIT_AND_MULTIQC.nf b/src/sub_workflows/MODKIT_AND_MULTIQC.nf
similarity index 100%
rename from sub_workflows/MODKIT_AND_MULTIQC.nf
rename to src/sub_workflows/MODKIT_AND_MULTIQC.nf