revert changes to the mnnpy component since it requires python:3.8 (#466

)

src/tasks/batch_integration/methods/mnnpy/config.vsh.yaml

@@ -30,8 +30,6 @@ functionality:
   resources:
     - type: python_script
       path: script.py
-    - type: python_script
-      path: /src/common/helper_functions/read_anndata_partial.py
 platforms:
   # Due to a [ gcc-8 ] dependency in the mnnpy package, we need to use a python:3.8 image
   - type: docker
@@ -51,4 +49,4 @@ platforms:
           - chriscainx/mnnpy
   - type: nextflow
     directives:
-      label: [midtime, lowcpu, lowmem]
+      label: [ midtime, lowcpu, lowmem ]

src/tasks/batch_integration/methods/mnnpy/script.py

@@ -1,4 +1,3 @@
-import sys
 import anndata as ad
 import mnnpy
 
@@ -14,18 +13,11 @@
 }
 ## VIASH END
 
-sys.path.append(meta["resources_dir"])
-from read_anndata_partial import read_anndata
-
-
 print('Read input', flush=True)
-adata = read_anndata(
-    par['input'],
-    X='layers/normalized',
-    obs='obs',
-    var='var',
-    uns='uns'
-)
+adata = ad.read_h5ad(par['input'])
+adata.X = adata.layers['normalized']
+del adata.layers['normalized']
+del adata.layers['counts']
 
 if par['n_hvg']:
     print(f"Select top {par['n_hvg']} high variable genes", flush=True)