Pin Seurat to v4

CHANGELOG.md

@@ -24,6 +24,8 @@
 
 ## MINOR CHANGES
 
+* Pin `from_h5mu_to_seurat` to use Seurat to version 4 (PR #630).
+
 * Refactored `rna_multisample` pipeline to use `fromState` and `toState` functionality (PR #607).
 
 * Refactored `cellranger_multi` workflow to use `fromState` and `toState` functionality (PR #609).

src/convert/from_h5mu_to_seurat/config.vsh.yaml

@@ -34,7 +34,7 @@ functionality:
   test_resources:
     - type: r_script
       path: run_test.R
-    - path: /resources_test/pbmc_1k_protein_v3
+    - path: /resources_test/10x_5k_anticmv/
 platforms:
   - type: docker
     image: eddelbuettel/r2u:22.04
@@ -53,7 +53,11 @@ platforms:
       - type: r
         cran: [ anndata, hdf5r, testthat ]
       - type: r
-        github: pmbio/MuDataSeurat
+        url: https://cran.r-project.org/src/contrib/Archive/SeuratObject/SeuratObject_4.0.2.tar.gz
+      - type: r
+        url: https://cran.r-project.org/src/contrib/Archive/Seurat/Seurat_4.0.4.tar.gz
+      - type: r
+        github: pmbio/MuDataSeurat@empty-tables-and-nullable
   - type: nextflow
     directives:
       label: [lowmem, singlecpu]

src/convert/from_h5mu_to_seurat/run_test.R

@@ -10,7 +10,7 @@ meta <- list(
 
 cat("> Checking whether output is correct\n")
 
-in_h5mu <- paste0(meta[["resources_dir"]], "/pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu")
+in_h5mu <- paste0(meta[["resources_dir"]], "/10x_5k_anticmv/5k_human_antiCMV_T_TBNK_connect_mms.h5mu")
 out_rds <- "output.rds"
 
 cat("> Running ", meta[["functionality_name"]], "\n", sep = "")
@@ -31,7 +31,7 @@ obj <- readRDS(file = out_rds)
 
 cat("> Checking whether Seurat object is in the right format\n")
 expect_is(obj, "Seurat")
-expect_equal(sort(names(slot(obj, "assays"))), sort(c("prot", "rna")))
+expect_equal(sort(names(slot(obj, "assays"))), sort(c("prot", "rna", "vdj_t")))
 
 obj_rna <- slot(obj, "assays")$rna
 obj_prot <- slot(obj, "assays")$prot