Re-enable from_h5mu_to_seurat component (#616)

* Re-enable from_h5mu_to_seurat component

* Add PR number

* update test

* add print statements

* change input file

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

Author: 2 people

CHANGELOG.md

@@ -18,6 +18,8 @@
 
 * `rna_multisample` workflow: added `--modality` argument (PR #607).
 
+* Re-enable `convert/from_h5mu_to_seurat` component (PR #616).
+
 ## MINOR CHANGES
 
 * Refactored `rna_multisample` pipeline to use `fromState` and `toState` functionality (PR #607).

src/base/requirements/anndata.yaml

@@ -0,0 +1,3 @@
+
+packages:
+  - anndata~=0.9.1

src/base/requirements/anndata_mudata.yaml

@@ -1,5 +1,4 @@
-
+__merge__: [/src/base/requirements/anndata.yaml, .]
 packages:
   - mudata~=0.2.3
-  - anndata~=0.9.1
   - pandas!=2.1.2

src/convert/from_h5mu_to_seurat/config.vsh.yaml

@@ -1,7 +1,5 @@
 functionality:
   name: "from_h5mu_to_seurat"
-  # MuDataSeurat is currently broken -- https://github.com/PMBio/MuDataSeurat/issues/9
-  status: disabled 
   namespace: "convert"
   description: |
     Converts an h5mu file into a Seurat file.
@@ -51,9 +49,7 @@ platforms:
           - python3-pip
           - python-is-python3
       - type: python
-        __merge__: [/src/base/requirements/scanpy.yaml, .]
-        packages: 
-          - anndata~=0.9.1
+        __merge__: [/src/base/requirements/scanpy.yaml, /src/base/requirements/anndata.yaml, .]
       - type: r
         cran: [ anndata, hdf5r, testthat ]
       - type: r

src/convert/from_h5mu_to_seurat/run_test.R

@@ -1,21 +1,31 @@
 library(testthat, warn.conflicts = FALSE)
 
-cat("Checking whether output is correct\n")
+## VIASH START
+meta <- list(
+  executable = "target/docker/convert/from_h5mu_to_seurat/from_h5mu_to_seurat",
+  resources_dir = "resources_test",
+  functionality_name = "from_h5mu_to_seurat"
+)
+## VIASH END
+
+cat("> Checking whether output is correct\n")
 
-# TODO: this should also work for ums and mms, but it doesn't.
-in_h5mu <- paste0(meta[["resources_dir"]], "/pbmc_1k_protein_v3/pbmc_1k_protein_v3_uss.h5mu")
+in_h5mu <- paste0(meta[["resources_dir"]], "/pbmc_1k_protein_v3/pbmc_1k_protein_v3_mms.h5mu")
 out_rds <- "output.rds"
 
 cat("> Running ", meta[["functionality_name"]], "\n", sep = "")
 out <- processx::run(
-  paste0("./", meta[["functionality_name"]]),
-  c("--input", in_h5mu, "--output", out_rds)
+  meta[["executable"]],
+  c(
+    "--input", in_h5mu,
+    "--output", out_rds
+  )
 )
 
 cat("> Checking whether output file exists\n")
 expect_equal(out$status, 0)
 expect_true(file.exists(out_rds))
-  
+
 cat("> Reading output file\n")
 obj <- readRDS(file = out_rds)
 

src/convert/from_h5mu_to_seurat/script.R

@@ -7,6 +7,8 @@ par <- list(
 )
 ## VIASH END
 
+cat("Reading input file\n")
 obj <- ReadH5MU(par$input)
 
+cat("Writing output file\n")
 saveRDS(obj, file = par$output, compress = TRUE)