Migrate to anndataR for adata_tords

Author: nictru

modules/local/adata/tords/environment.yml

@@ -1,8 +1,5 @@
-name: adata_tords
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::anndata2ri=1.3.2
-  - conda-forge::anndata=0.11.1
-  - conda-forge::r-seurat=5.1.0
+  - bioconda::bioconductor-anndatar=1.0.2

modules/local/adata/tords/main.nf

@@ -4,8 +4,8 @@ process ADATA_TORDS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/anndata2ri_bioconductor-singlecellexperiment_anndata_r-seurat:c4b75a61a89ec006':
-        'community.wave.seqera.io/library/anndata2ri_bioconductor-singlecellexperiment_anndata_r-seurat:5fae42aabf7a1c5f' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9e/9e2d0625efb46bae98303a0e685efa0ee259b939a6490eef13218c16c601bc9b/data':
+        'community.wave.seqera.io/library/bioconductor-anndatar_bioconductor-rhdf5_bioconductor-singlecellexperiment:b7b9571d025f377e' }"
 
     input:
     tuple val(meta), path(h5ad)
@@ -20,7 +20,7 @@ process ADATA_TORDS {
     script:
     counts_layer = task.ext.counts_layer ?: 'X'
     prefix = task.ext.prefix ?: "${meta.id}"
-    template 'tords.py'
+    template 'tords.R'
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"

modules/local/adata/tords/templates/tords.R

@@ -0,0 +1,24 @@
+#!/usr/bin/env Rscript
+
+library(anndataR)
+
+counts_layer <- "${counts_layer}"
+prefix <- "${prefix}"
+h5ad <- "${h5ad}"
+
+adata <- read_h5ad(h5ad)
+sce <- adata\$as_SingleCellExperiment()
+
+SummarizedExperiment::assayNames(sce)[SummarizedExperiment::assayNames(sce) == counts_layer] <- "counts"
+
+saveRDS(sce, paste0(prefix, ".rds"))
+
+ver <- packageVersion("anndataR")
+
+writeLines(
+    c(
+        "${task.process}:",
+        paste0("    anndataR: ", ver)
+    ),
+    "versions.yml"
+)

modules/local/adata/tords/templates/tords.py

@@ -26,11 +26,11 @@
                 ]
             }
         ],
+        "timestamp": "2025-06-01T21:20:06.728038404",
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "25.04.2"
-        },
-        "timestamp": "2025-06-01T21:20:06.728038404"
+        }
     },
     "Should run without failures": {
         "content": [
@@ -40,29 +40,29 @@
                         {
                             "id": "test"
                         },
-                        "test.rds:md5,49e4f1ab25d434c507b5e07d0dd40c5d"
+                        "test.rds:md5,ba065e9d68612a96bcc95eba7ff84da4"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,49dc8f6638973bec2c328ee45dca2137"
+                    "versions.yml:md5,bf93dcd42995e7fa34eac37384568f9d"
                 ],
                 "rds": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.rds:md5,49e4f1ab25d434c507b5e07d0dd40c5d"
+                        "test.rds:md5,ba065e9d68612a96bcc95eba7ff84da4"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,49dc8f6638973bec2c328ee45dca2137"
+                    "versions.yml:md5,bf93dcd42995e7fa34eac37384568f9d"
                 ]
             }
         ],
+        "timestamp": "2026-03-14T21:05:44.197188707",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
-        },
-        "timestamp": "2025-07-13T20:42:25.313956328"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }