From a972170a3d973b39995990c43372e9a95ba71c55 Mon Sep 17 00:00:00 2001
From: Quentin Blampey <quentin.blampey@gmail.com>
Date: Mon, 20 Jan 2025 18:19:18 +0100
Subject: [PATCH] remove current VHD smk config - should use stardist (WIP)

---
 workflow/config/visium_hd/cellpose.yaml | 21 ---------------------
 1 file changed, 21 deletions(-)
 delete mode 100644 workflow/config/visium_hd/cellpose.yaml

diff --git a/workflow/config/visium_hd/cellpose.yaml b/workflow/config/visium_hd/cellpose.yaml
deleted file mode 100644
index caadbf14..00000000
--- a/workflow/config/visium_hd/cellpose.yaml
+++ /dev/null
@@ -1,21 +0,0 @@
-# For parameters details, see this commented example: https://github.com/gustaveroussy/sopa/blob/master/workflow/config/example_commented.yaml
-read:
-  technology: visium_hd
-
-patchify:
-  patch_width_pixel: 2000
-  patch_overlap_pixel: 50
-
-segmentation:
-  cellpose:
-    diameter: 15
-    channels: ["r"] # first channel of the H&E image
-    min_area: 50
-
-aggregate:
-  aggregate_channels: false
-  aggregate_genes: true
-  min_transcripts: 10 # [optional] cells whose transcript count is below that this threshold are filtered
-
-explorer:
-  ram_threshold_gb: 4