Explicitly set var and obs columns while filtering with counts. (open…

…pipelines-bio#262)

* Explicitly set var and obs columns while filtering with counts

* Add CHANGELOG

CHANGELOG.md

@@ -13,6 +13,8 @@ These options were previously covered in the `bin/init` script, but this new fea
 
 * `filter/do_filter`: resolved an issue where the .obs column instead of the .var column was being logged when filtering using the .var column.
 
+* `workflows/rna_singlesample` and `workflows/prot_singlesample`: Correctly set var and obs columns while filtering with counts.
+
 * `filter/do_filter`: removed the default input value for `var_filter` argument.
 
 # openpipelines 0.6.2

workflows/multiomics/prot_singlesample/main.nf

@@ -41,11 +41,20 @@ workflow run_wf {
     // filtering
     | getWorkflowArguments(key: "filter_with_counts")
     | filter_with_counts.run(
-        args: [ var_gene_names: "gene_symbol", modality: "prot"]
+        args: [ 
+          var_gene_names: "gene_symbol",
+          modality: "prot", 
+          obs_name_filter: "filter_with_counts",
+          var_name_filter: "filter_with_counts"
+        ]
     )
     | getWorkflowArguments(key: "do_filter")
     | do_filter.run(
-      args: [ obs_filter: "filter_with_counts", modality: "prot" ]
+        args: [
+          obs_filter: "filter_with_counts",
+          modality: "prot",
+          var_filter: "filter_with_counts"
+        ]
     )
     | map {list -> [list[0], list[1]] + list.drop(3)}
     | view { "Output: $it" }

workflows/multiomics/rna_singlesample/main.nf

@@ -45,11 +45,18 @@ workflow run_wf {
     // cell filtering
     | getWorkflowArguments(key: "filter_with_counts")
     | filter_with_counts.run(
-        args: [ var_gene_names: "gene_symbol" ]
+        args: [
+          var_gene_names: "gene_symbol",
+          obs_name_filter: "filter_with_counts", 
+          var_name_filter: "filter_with_counts"
+        ]
     )
     | getWorkflowArguments(key: "do_filter")
     | do_filter.run(
-      args: [ obs_filter: "filter_with_counts" ]
+      args: [
+        obs_filter: "filter_with_counts",
+        var_filter: "filter_with_counts"
+      ]
     )
     // doublet calling
     | getWorkflowArguments(key: "filter_with_scrublet")