add cell hashing columns argument

Author: seohyonkim

modules/nf-core/hashsolo/main.nf

@@ -8,7 +8,7 @@ process HASHSOLO {
         'community.wave.seqera.io/library/scanpy:1.11.2--cc70dffaa98ddb98' }"
 
     input:
-    tuple val(meta), path(input_h5ad)
+    tuple val(meta), path(input_h5ad), val(cell_hashing_collumns)
     val params
 
     output:

modules/nf-core/hashsolo/meta.yml

@@ -27,6 +27,11 @@ input:
           correspond to cells and columns to genes.
         pattern: "*.h5ad"
         ontologies: []
+    - cell_hashing_collumns:
+        type: list
+        description: |
+          List of cell hashing columns to use for demultiplexing.
+          e.g. `['hash_1', 'hash_2']`
   - - params:
         type: map
         description: Parameters for hashsolo.

modules/nf-core/hashsolo/templates/hashsolo.py

@@ -12,5 +12,5 @@
     params = {}
 
 adata = sc.read_h5ad("${input_h5ad}")
-sce.pp.hashsolo(adata, "${params}")
+sce.pp.hashsolo(adata, "${cell_hashing_columns}","${params}")
 adata.write("test/${prefix}_hashsolo.h5ad")

modules/nf-core/hashsolo/tests/main.nf.test

@@ -16,6 +16,7 @@ nextflow_process {
                 input[0] = [
                     [ id: 'test' ], // meta map
                     file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/cellranger/hashing_demultiplexing/hashsolo_anndata.h5ad', checkIfExists: true),
+                    ["Hash1", "Hash2", "Hash3"]
                 ]
 
                 input[1] = '' // pass nothing