Revert convert subworkflow change

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
+}