Update counts_layer usage

Author: nictru

modules/local/adata/tords/main.nf

@@ -9,6 +9,7 @@ process ADATA_TORDS {
 
     input:
     tuple val(meta), path(h5ad)
+    val counts_layer
 
     output:
     tuple val(meta), path("*.rds"), emit: rds
@@ -18,7 +19,7 @@ process ADATA_TORDS {
     task.ext.when == null || task.ext.when
 
     script:
-    counts_layer = task.ext.counts_layer ?: 'X'
+    counts_layer = counts_layer ?: 'X'
     prefix = task.ext.prefix ?: "${meta.id}"
     template 'tords.R'
 

modules/local/adata/tords/tests/main.nf.test

@@ -20,6 +20,7 @@ nextflow_process {
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/h5ad/SRR28679756_filtered_matrix.h5ad', checkIfExists: true)
                     ]
                 )
+                input[1] = 'X'
                 """
             }
         }
@@ -48,6 +49,7 @@ nextflow_process {
                         file(params.modules_testdata_base_path + 'genomics/homo_sapiens/scrnaseq/h5ad/SRR28679756_filtered_matrix.h5ad', checkIfExists: true)
                     ]
                 )
+                input[1] = 'X'
                 """
             }
         }

subworkflows/local/finalize/main.nf

@@ -27,7 +27,8 @@ workflow FINALIZE {
     ch_versions = ch_versions.mix(ADATA_EXTEND.out.versions)
 
     ADATA_TORDS (
-        ADATA_EXTEND.out.h5ad
+        ADATA_EXTEND.out.h5ad,
+        'X'
     )
     ch_versions = ch_versions.mix(ADATA_TORDS.out.versions)