From 17a94a8ef0b78f8b728c2fe0425147c1a657709f Mon Sep 17 00:00:00 2001 From: Luke Zappia Date: Mon, 23 Jun 2025 09:30:43 +0200 Subject: [PATCH] Update anndata_convert script --- modules/local/templates/anndatar_convert.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/templates/anndatar_convert.R b/modules/local/templates/anndatar_convert.R index 6f78e282..4d710258 100755 --- a/modules/local/templates/anndatar_convert.R +++ b/modules/local/templates/anndatar_convert.R @@ -11,14 +11,14 @@ library(SingleCellExperiment) adata <- read_h5ad("${h5ad}") # convert to Seurat -obj <- adata\$to_Seurat() +obj <- adata\$as_Seurat() # save files dir.create(file.path("$meta.id"), showWarnings = FALSE) saveRDS(obj, file = "${meta.id}_${meta.input_type}_matrix.seurat.rds") # convert to SingleCellExperiment -obj <- adata\$to_SingleCellExperiment() +obj <- adata\$as_SingleCellExperiment() # save files dir.create(file.path("$meta.id"), showWarnings = FALSE)