Merge pull request #225 from nf-core/ambient

Improve ambient RNA implementation

Author: nictru

assets/schema_input.json

@@ -115,6 +115,17 @@
                 "default": 0,
                 "errorMessage": "Number of cells expected from the experimental design, used as input to cellbender.",
                 "meta": ["expected_cells"]
+            },
+            "ambient_correction": {
+                "type": "boolean",
+                "default": true,
+                "errorMessage": "'ambient_correction' must be a boolean.",
+                "meta": ["ambient_correction"]
+            },
+            "ambient_corrected_integration": {
+                "type": "boolean",
+                "errorMessage": "'ambient_corrected_integration' must be a boolean.",
+                "meta": ["ambient_corrected_integration"]
             }
         },
         "anyOf": [

conf/modules.config

@@ -139,7 +139,6 @@ process {
 
     withName: '.*:AMBIENT_RNA_REMOVAL:CELLBENDER_MERGE' {
         ext.prefix       = { meta.id + '_cellbender' }
-        ext.output_layer = 'ambient'
         publishDir       = [
             path: { "${params.outdir}/quality_control/ambient_rna_removal" },
             mode: params.publish_dir_mode,

docs/usage.md

@@ -18,7 +18,8 @@
                     "cellbender/merge": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/cellbender/merge/cellbender-merge.diff"
                     },
                     "cellbender/removebackground": {
                         "branch": "master",
@@ -43,7 +44,8 @@
                     "scvitools/scar": {
                         "branch": "master",
                         "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/scvitools/scar/scvitools-scar.diff"
                     },
                     "scvitools/solo": {
                         "branch": "master",

modules.json

@@ -8,6 +8,7 @@ process CELDA_DECONTX {
     tuple val(meta), path(h5ad), path(raw)
     val(batch_col)
     val(input_layer)
+    val(output_layer)
 
     output:
     tuple val(meta), path("*.h5ad"), emit: h5ad
@@ -18,7 +19,6 @@ process CELDA_DECONTX {
 
     script:
     prefix = task.ext.prefix ?: "${meta.id}"
-    output_layer = task.ext.output_layer ?: "decontXcounts"
     template 'decontx.R'
 
     stub:

modules/local/celda/decontx/main.nf

@@ -32,7 +32,11 @@ corrected <- do.call(decontX, c(list(sce), params))
 adata_corrected <- as_AnnData(corrected)
 
 # Convert back to AnnData and update layers
-adata\$layers["${output_layer}"] <- adata_corrected\$layers["decontXcounts"]
+if ("${output_layer}" == "X") {
+    adata\$X <- adata_corrected\$layers[["decontXcounts"]]
+} else {
+    adata\$layers[["${output_layer}"]] <- adata_corrected\$layers[["decontXcounts"]]
+}
 
 # Save the output
 write_h5ad(adata, "${prefix}.h5ad")

modules/local/celda/decontx/templates/decontx.R

@@ -23,6 +23,7 @@ nextflow_process {
                 )
                 input[1] = "sample"
                 input[2] = "X"
+                input[3] = "X"
                 """
             }
         }
@@ -57,6 +58,7 @@ nextflow_process {
                 )
                 input[1] = "sample"
                 input[2] = "X"
+                input[3] = "X"
                 """
             }
         }
@@ -91,6 +93,7 @@ nextflow_process {
                 )
                 input[1] = "sample"
                 input[2] = "X"
+                input[3] = "X"
                 """
             }
         }
@@ -120,6 +123,7 @@ nextflow_process {
                 )
                 input[1] = "sample"
                 input[2] = "X"
+                input[3] = "X"
                 """
             }
         }
@@ -155,6 +159,7 @@ nextflow_process {
                 )
                 input[1] = "sample"
                 input[2] = "X"
+                input[3] = "X"
                 """
             }
         }

modules/local/celda/decontx/tests/main.nf.test

@@ -18,13 +18,13 @@
                 "versions.yml:md5,c546ef8ddb5673ef5f14e733d02de1d1"
             ],
             true,
-            20467768
+            14391284
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-07-13T20:47:56.707357668"
+        "timestamp": "2025-08-31T13:29:55.8622939"
     },
     "Should run without failures with raw - stub": {
         "content": [

modules/local/celda/decontx/tests/main.nf.test.snap

@@ -6,7 +6,9 @@ process SOUPX {
 
     input:
     tuple val(meta), path(h5ad), path(raw)
+    val(cluster_resolution)
     val(input_layer)
+    val(output_layer)
 
     output:
     tuple val(meta), path("${prefix}.h5ad"), emit: h5ad
@@ -17,8 +19,6 @@ process SOUPX {
 
     script:
     prefix = task.ext.prefix ?: "${meta.id}"
-    cluster_resolution = task.ext.cluster_resolution ?: 0.8
-    output_layer = task.ext.output_layer ?: "ambient_corrected"
     template 'soupx.R'
 
     stub:

modules/local/soupx/main.nf

@@ -57,7 +57,11 @@ sc <- autoEstCont(sc, doPlot = FALSE)
 out <- adjustCounts(sc, roundToInt = FALSE)
 
 # Update the original AnnData object with ambient layer
-adata\$layers[["${output_layer}"]] <- t(out)
+if ("${output_layer}" == "X") {
+    adata\$X <- t(out)
+} else {
+    adata\$layers[["${output_layer}"]] <- t(out)
+}
 
 # Save the output
 write_h5ad(adata, "${prefix}.h5ad")