Port 0.12.1 changes to main (#615)

openpipelines-bio · Nov 14, 2023 · 27e74d9 · 27e74d9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -26,6 +26,13 @@
 
 * Refactored `cellranger_mapping` workflow to use `fromState` and `toState` functionality (PR #610).
 
+# openpipelines 0.12.1
+
+## BUG FIXES
+
+* `rna_singlesample`: Fix filtering parameters values `min_counts`, `max_counts`, `min_genes_per_cell`, `max_genes_per_cell` and `min_cells_per_gene` not being passed to the `filter_with_counts` component (PR #614).
+
+* `prot_singlesample`: Fix filtering parameters values `min_counts`, `max_counts`, `min_proteins_per_cell`, `max_proteins_per_cell` and `min_cells_per_protein` not being passed to the `filter_with_counts` component (PR #614).
 
 # openpipelines 0.12.0
 

diff --git a/src/workflows/multiomics/prot_singlesample/main.nf b/src/workflows/multiomics/prot_singlesample/main.nf
@@ -55,8 +55,6 @@ workflow run_wf {
           "min_genes_per_cell": "min_proteins_per_cell",
           "max_genes_per_cell": "max_proteins_per_cell",
           "min_cells_per_gene": "min_cells_per_protein",
-          "min_fraction_mito": "min_fraction_mito",
-          "max_fraction_mito": "max_fraction_mito",
           "workflow_output": "workflow_output"
       ]
       def new_state = stateMapping.collectEntries{newKey, origKey ->
@@ -70,6 +68,11 @@ workflow run_wf {
       fromState: { id, state ->
         [
           "input": state.input,
+          "min_counts": state.min_counts,
+          "max_counts": state.max_counts,
+          "min_genes_per_cell": state.min_proteins_per_cell,
+          "max_genes_per_cell": state.max_proteins_per_cell,
+          "min_cells_per_gene": state.min_cells_per_protein,
           "obs_name_filter": "filter_with_counts",
           "var_name_filter": "filter_with_counts",
           "modality": "prot"
@@ -81,9 +84,9 @@ workflow run_wf {
       fromState : { id, state ->
         [
           "input": state.input,
-          "obs_filter": state.filter_with_counts,
+          "obs_filter": "filter_with_counts",
           "modality": "prot",
-          "var_filter": state.filter_with_counts,
+          "var_filter": "filter_with_counts",
           "output_compression": "gzip",
           "output": state.workflow_output
         ]

diff --git a/src/workflows/multiomics/rna_singlesample/main.nf b/src/workflows/multiomics/rna_singlesample/main.nf
@@ -99,6 +99,12 @@ workflow run_wf {
         "var_name_mitochondrial_genes": "var_name_mitochondrial_genes",
         "workflow_output": "workflow_output"
       ]
+      if (orig_state.min_fraction_mito) {
+        stateMapping += ["min_fraction_mito": "min_fraction_mito"]
+      }
+      if (orig_state.max_fraction_mito) {
+        stateMapping += ["max_fraction_mito": "max_fraction_mito"] 
+      }
       def new_state = stateMapping.collectEntries{newKey, origKey ->
         [newKey, orig_state[origKey]]
       }
@@ -113,6 +119,8 @@ workflow run_wf {
         [
           "input": state.input,
           "obs_name_filter": "filter_mitochondrial",
+          "min_fraction": state.min_fraction_mito,
+          "max_fraction": state.max_fraction_mito,
           "obs_fraction_column": "fraction_$state.var_name_mitochondrial_genes"
         ]
       },
@@ -128,12 +136,16 @@ workflow run_wf {
         [
           "input": state.input,
           "obs_name_filter": "filter_with_counts",
-          "var_name_filter": "filter_with_counts"
+          "var_name_filter": "filter_with_counts",
+          "min_counts": state.min_counts,
+          "max_counts": state.max_counts,
+          "min_genes_per_cell": state.min_genes_per_cell,
+          "max_genes_per_cell": state.max_genes_per_cell,
+          "min_cells_per_gene": state.min_cells_per_gene,
         ]
       },
       toState: ["input": "output"]
     )
-    | view {"before filter: $it"}
     | do_filter.run(
       fromState: {id, state ->
         def stateMapping = [