diff --git a/subworkflows/local/convert.nf b/subworkflows/local/convert.nf
new file mode 100644
index 0000000..71031e9
--- /dev/null
+++ b/subworkflows/local/convert.nf
@@ -0,0 +1,56 @@
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    IMPORT LOCAL MODULES
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+include { CONVERT_ADAPTIVE }                from '../../modules/local/convert/convert_adaptive'
+include { PSEUDOBULK_CELLRANGER }           from '../../modules/local/convert/pseudobulk_cellranger'
+include { PSEUDOBULK_PHENOTYPE_CELLRANGER } from '../../modules/local/convert/pseudobulk_phenotype_cellranger'
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    RUN MAIN SUBWORKFLOW
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+workflow CONVERT {
+    take:
+    sample_map
+    input_format
+
+    main:    
+    pseudobulk_phenotype_files = channel.empty() // Initialize empty channel for phenotype files
+
+    if (input_format == 'adaptive') {
+        CONVERT_ADAPTIVE(
+            sample_map,
+            file(params.airr_schema),
+            file(params.imgt_lookup)
+        )
+        sample_map_converted = CONVERT_ADAPTIVE.out.adaptive_convert
+
+    } else if (input_format == 'cellranger') {
+        PSEUDOBULK_CELLRANGER(
+            sample_map,
+            file(params.airr_schema)
+        )
+        sample_map_converted = PSEUDOBULK_CELLRANGER.out.cellranger_pseudobulk
+
+        if (params.sobject_gex) {
+            PSEUDOBULK_PHENOTYPE_CELLRANGER(
+                sample_map,
+                file(params.airr_schema),
+                file(params.sobject_gex)
+            )
+            pseudobulk_phenotype_files = PSEUDOBULK_PHENOTYPE_CELLRANGER.out.cellranger_pseudobulk_phenotype
+        }
+    } else {
+        sample_map_converted = sample_map
+    }
+
+    emit:
+    sample_map_converted
+    pseudobulk_phenotype_files
+}
\ No newline at end of file
diff --git a/subworkflows/local/convert/adaptive.nf b/subworkflows/local/convert/adaptive.nf
deleted file mode 100644
index 31980e5..0000000
--- a/subworkflows/local/convert/adaptive.nf
+++ /dev/null
@@ -1,16 +0,0 @@
-include { CONVERT_ADAPTIVE } from '../../../modules/local/convert/convert_adaptive'
-
-workflow ADAPTIVE {
-    take:
-    sample_map
-
-    main:    
-    CONVERT_ADAPTIVE(
-        sample_map,
-        params.airr_schema,
-        params.imgt_lookup
-    )
-
-    emit:
-    CONVERT_ADAPTIVE.out.adaptive_convert
-}
\ No newline at end of file
diff --git a/subworkflows/local/convert/main.nf b/subworkflows/local/convert/main.nf
deleted file mode 100644
index 5e0fb8c..0000000
--- a/subworkflows/local/convert/main.nf
+++ /dev/null
@@ -1,45 +0,0 @@
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT LOCAL MODULES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-include { ADAPTIVE } from './adaptive'
-include { PSEUDOBULK } from './pseudobulk_cellranger'
-include { PSEUDOBULK_PHENOTYPE } from './pseudobulk_phenotype'
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN MAIN SUBWORKFLOW
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-workflow CONVERT {
-    take:
-    sample_map
-    input_format
-
-    main:    
-    ch_pseudobulk_phenotype = channel.empty() // Initialize empty channel for phenotype files
-
-    if (input_format == 'adaptive') {
-        ADAPTIVE(sample_map)
-        sample_map_converted = ADAPTIVE.out
-    } else if (input_format == 'cellranger') {
-        PSEUDOBULK(sample_map)
-        sample_map_converted = PSEUDOBULK.out
-
-        if (params.sobject_gex) {
-            PSEUDOBULK_PHENOTYPE(
-                sample_map,
-                file(params.sobject_gex)
-            )
-            ch_pseudobulk_phenotype = PSEUDOBULK_PHENOTYPE.out.ch_pseudobulk_phenotype
-        }
-    }
-
-    emit:
-    sample_map_converted
-    pseudobulk_phenotype_files = ch_pseudobulk_phenotype
-}
\ No newline at end of file
diff --git a/subworkflows/local/convert/pseudobulk_cellranger.nf b/subworkflows/local/convert/pseudobulk_cellranger.nf
deleted file mode 100644
index 174d990..0000000
--- a/subworkflows/local/convert/pseudobulk_cellranger.nf
+++ /dev/null
@@ -1,15 +0,0 @@
-include { PSEUDOBULK_CELLRANGER } from '../../../modules/local/convert/pseudobulk_cellranger'
-
-workflow PSEUDOBULK {
-    take:
-    sample_map
-
-    main:    
-    PSEUDOBULK_CELLRANGER(
-        sample_map,
-        params.airr_schema,
-    )
-
-    emit:
-    PSEUDOBULK_CELLRANGER.out.cellranger_pseudobulk
-}
\ No newline at end of file
diff --git a/subworkflows/local/convert/pseudobulk_phenotype.nf b/subworkflows/local/convert/pseudobulk_phenotype.nf
deleted file mode 100644
index 4ada72c..0000000
--- a/subworkflows/local/convert/pseudobulk_phenotype.nf
+++ /dev/null
@@ -1,17 +0,0 @@
-include { PSEUDOBULK_PHENOTYPE_CELLRANGER } from '../../../modules/local/convert/pseudobulk_phenotype_cellranger'
-
-workflow PSEUDOBULK_PHENOTYPE {
-    take:
-    sample_map
-    sobject_gex
-
-    main:    
-    PSEUDOBULK_PHENOTYPE_CELLRANGER(
-        sample_map,
-        params.airr_schema,
-        sobject_gex
-    )
-
-    emit:
-    PSEUDOBULK_PHENOTYPE_CELLRANGER.out.cellranger_pseudobulk_phenotype
-}
\ No newline at end of file