Make cell type mappings file really optional

nextflow.config

@@ -30,7 +30,7 @@ params {
     input = './refs/SampleSheet.tsv'
     ensembl_mappings = './src/ensembl-ids/ensembl_mappings.tsv'
     ctd_path = 'https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/28033407/ctd_v1.zip'
-    celltype_mappings = './conf/celltype_mappings.tsv'
+    celltype_mappings = null
     reddim_genes_yml = './conf/reddim_genes.yml'
 
     // Boilerplate options

nextflow_schema.json

@@ -38,7 +38,6 @@
                 },
                 "celltype_mappings": {
                     "type": "string",
-                    "default": "./conf/celltype_mappings.tsv",
                     "fa_icon": "fas fa-table",
                     "description": "Optional tsv file specifying manual revisions of cell-type annotations."
                 },
@@ -1480,4 +1479,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}

workflows/scflow.nf

@@ -321,28 +321,30 @@ workflow SCFLOW {
         ch_ctd_path
     )
 
-    SCFLOW_FINALIZE (
-        SCFLOW_MAPCELLTYPES.out.celltype_mapped_sce,
-        ch_celltype_mappings
-    )
+    if (params.celltype_mappings) {
+        SCFLOW_FINALIZE (
+            SCFLOW_MAPCELLTYPES.out.celltype_mapped_sce,
+            ch_celltype_mappings
+        )
 
-    SCFLOW_DGE (
-        SCFLOW_FINALIZE.out.final_sce,
-        params.dge_de_method,
-        SCFLOW_FINALIZE.out.celltypes.splitCsv (
-            header:['celltype', 'n_cells'], skip: 1, sep: '\t'
+        SCFLOW_DGE (
+            SCFLOW_FINALIZE.out.final_sce,
+            params.dge_de_method,
+            SCFLOW_FINALIZE.out.celltypes.splitCsv (
+                header:['celltype', 'n_cells'], skip: 1, sep: '\t'
+            )
+            .map { row -> tuple(row.celltype, row.n_cells) },
+            ch_ensembl_mappings3
         )
-        .map { row -> tuple(row.celltype, row.n_cells) },
-        ch_ensembl_mappings3
-    )
 
-    SCFLOW_IPA (
-        SCFLOW_DGE.out.de_table
-    )
+        SCFLOW_IPA (
+            SCFLOW_DGE.out.de_table
+        )
 
-    SCFLOW_DIRICHLET (
-        SCFLOW_FINALIZE.out.final_sce
-    )
+        SCFLOW_DIRICHLET (
+            SCFLOW_FINALIZE.out.final_sce
+        )
+    }
 
     SCFLOW_PLOTREDDIMGENES (
         SCFLOW_CLUSTER.out.clustered_sce,