modify emptydrops ambiguous mentions for cellbender remove background

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add profile for gpu processes ([#419](https://github.com/nf-core/scrnaseq/pull/419/))
 - Update example usage command in README with valid reference genome parameter ([#339](https://github.com/nf-core/scrnaseq/issues/339))
 - Removed `--kb_filter` parameter. Kallisto filtering is triggered by default and can be turned off with `ext.args` ([#421](https://github.com/nf-core/scrnaseq/issues/421))
+- Document better that `cellbender` is used for empty drops calling and not the `emptydrops` method (([#420](https://github.com/nf-core/scrnaseq/issues/420)))
 
 ## v3.0.0 - 2024-12-09
 

conf/modules.config

@@ -31,10 +31,10 @@ process {
         ]
     }
 
-    if (!params.skip_emptydrops) {
+    if (!params.skip_cellbender) {
         withName: 'CELLBENDER_REMOVEBACKGROUND' {
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}/${meta.id}/emptydrops_filter" },
+                path: { "${params.outdir}/${params.aligner}/${meta.id}/cellbender_removebackground" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]

conf/test.config

@@ -24,7 +24,7 @@ params {
 
     // Input data
     input           = 'https://github.com/nf-core/test-datasets/raw/scrnaseq/samplesheet-2-0.csv'
-    skip_emptydrops = true // module does not work on small dataset
+    skip_cellbender = true // module does not work on small dataset
 
     // Genome references
     fasta        = 'https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa'

conf/test_cellranger_multi.config

@@ -33,7 +33,7 @@ params {
     cellranger_multi_barcodes = "${projectDir}/assets/cellranger_barcodes_samplesheet.csv"
     gex_frna_probe_set        = "${projectDir}/assets/frna_probeset_subset.csv"
     fb_reference              = "${projectDir}/assets/fb_reference.csv"
-    skip_emptydrops           = true // not enough data in small test
+    skip_cellbender           = true // not enough data in small test
 
     // Genome references
     fasta           = 'https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.14.fa.gz'

docs/output.md

@@ -19,7 +19,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Cellranger](#cellranger)
 - [Cellranger ARC](#cellranger-arc)
 - [Cellranger multi](#cellranger-multi)
-- [Cellbender emptydrops filter](#cellbender-emptydrops-filter)
+- [Cellbender remove background filter](#cellbender-remove-background-filter)
 - [Other output data](#other-output-data)
 - [MultiQC](#multiqc)
 
@@ -124,15 +124,15 @@ for the corresponding documentation.
 - Overall same output structure as cellranger. In case of multiplexed samples there will be one ouput folder for
   each demultiplexed sample, and one containing all (non-demultiplexed) cells.
 
-## Cellbender emptydrops filter
+## Cellbender remove background filter
 
-The pipeline also possess a subworkflow imported from scdownstream to perform emptydrops calling and filtering using [cellbender](https://github.com/broadinstitute/CellBender). The process is simple, it takes a raw/unfiltered matrix file, and performs the emptydrops calling and filtering on it, generating another matrix file.
+The pipeline also possess a subworkflow imported from scdownstream to perform filter empty drops using [cellbender](https://github.com/broadinstitute/CellBender) remove background function. The process is simple, it takes a raw/unfiltered matrix file, and performs the filltering on it, generating another matrix file.
 
-> Users can turn it of with `--skip_emptydrops`.
+> Users can turn it of with `--skip_cellbender`.
 
-**Output directory: `results/${params.aligner}/${meta.id}/emptydrops_filter`**
+**Output directory: `results/${params.aligner}/${meta.id}/cellbender_removebackground`**
 
-- Contains the emptydrops filtered matrices results generated by the cellbender subworkflow.
+- Contains the cellbender filtered matrices results generated by the remove background functionality.
 
 ## Other output data
 
@@ -157,13 +157,13 @@ Because the pipeline has both the data directly from the aligners, and from the
 modified to understand the difference between raw/filtered from the aligners itself and filtered from the empty-drops module.
 So, to try to avoid confusion by the user, we added "suffixes" to the generated converted files so that we have provenance from what input it came from.
 
-So, the conversion modules generate data with the following syntax: **`*_{raw,filtered,emptydrops_filter}_matrix.{h5ad,rds}`**. With the following meanings:
+So, the conversion modules generate data with the following syntax: **`*_{raw,filtered,cellbender_filter}_matrix.{h5ad,rds}`**. With the following meanings:
 
 | suffix            | meaning                                                                                                                                  |
 | :---------------- | :--------------------------------------------------------------------------------------------------------------------------------------- |
 | raw               | Conversion of the raw/unprocessed matrix generated by the tool. It is also used for tools that generate only one matrix, such as alevin. |
 | filtered          | Conversion of the filtered/processed matrix generated by the tool                                                                        |
-| emptydrops_filter | Conversion of the matrix that was generated by the cellbender empty drops filter module                                                  |
+| cellbender_filter | Conversion of the matrix that was generated by the cellbender remove background filtering module                                         |
 
 > Some aligners, like `alevin` do not produce both raw&filtered matrices. When aligners give only one output, they are treated with the `raw` suffix.
 > Some aligners may have an option to give both raw&filtered and only one, like `kallisto`. Be aware when using the tools.

nextflow.config

@@ -50,7 +50,7 @@ params {
     cellrangerarc_reference = null
 
     // Emptydrops parameters
-    skip_emptydrops = false
+    skip_cellbender = false
 
     // CellrangerMulti parameters
     cellranger_vdj_index = null

nextflow_schema.json

@@ -88,7 +88,7 @@
                     "type": "boolean",
                     "description": "Skip FastQC"
                 },
-                "skip_emptydrops": {
+                "skip_cellbender": {
                     "type": "boolean",
                     "description": "Skip cellbender empty drops filter subworkflow"
                 }

tests/main_pipeline_cellrangermulti.nf.test

@@ -18,7 +18,7 @@ nextflow_pipeline {
                 gtf                       = 'https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens/Homo_sapiens.GRCh38.110.gtf.gz'
                 aligner                   = 'cellrangermulti'
                 protocol                  = 'auto'
-                skip_emptydrops           = true
+                skip_cellbender           = true
             }
         }
 

tests/nextflow.config

@@ -23,7 +23,7 @@ params {
     protocol     = '10XV2'
 
     // small dataset does not have sufficient data for emptydrops module
-    skip_emptydrops = true
+    skip_cellbender = true
 
     validationSchemaIgnoreParams = 'genomes'
 }

workflows/scrnaseq.nf

@@ -279,16 +279,16 @@ workflow SCRNASEQ {
     ch_h5ads = MTX_TO_H5AD.out.h5ad
 
     //
-    // SUBWORKFLOW: Run cellbender emptydrops filter
+    // SUBWORKFLOW: Run cellbender remove background subworkflow
     //
-    if ( !params.skip_emptydrops && !(params.aligner in ['cellrangerarc']) ) {
-        // emptydrops should only run on the raw matrices thus, filter-out the filtered result of the aligners that can produce it
+    if ( !params.skip_cellbender && !(params.aligner in ['cellrangerarc']) ) {
+        // module should only run on the raw matrices thus, filter-out the filtered result of the aligners that can produce it
         H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA (
             ch_h5ads.filter { meta, mtx_files -> meta.input_type == 'raw' }
         )
         ch_h5ads = ch_h5ads.mix(
             H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA.out.h5ad
-                .map{ meta, file -> [ meta + [input_type: 'emptydrops'], file ]}
+                .map{ meta, file -> [ meta + [input_type: 'cellbender_filter'], file ]}
         )
     }