From cbcf0d15bd8ed50dfd262f012cc1ea5410bdcad9 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Wed, 22 Mar 2023 16:19:24 +0000
Subject: [PATCH 1/2] Make cell type mappings file really optional

---
 workflows/scflow.nf | 38 ++++++++++++++++++++------------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/workflows/scflow.nf b/workflows/scflow.nf
index 9f27efd..3d1c317 100644
--- a/workflows/scflow.nf
+++ b/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,

From c09c1cb9ec30c968c317c2c50da1322c2aafe667 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@healx.io>
Date: Wed, 22 Mar 2023 16:24:59 +0000
Subject: [PATCH 2/2] Remove cell type mapping defaults

---
 nextflow.config      | 2 +-
 nextflow_schema.json | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 834c279..5c63b1b 100644
--- a/nextflow.config
+++ b/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
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f209156..368b61d 100644
--- a/nextflow_schema.json
+++ b/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"
         }
     ]
-}
\ No newline at end of file
+}