change skip_emptydrops to skip_cellbender

nf-core · Jan 20, 2025 · d5679c9 · d5679c9
1 parent 0316a79
commit d5679c9
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Showing 9 changed files with 9 additions and 9 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -31,7 +31,7 @@ process {
         ]
     }
 
-    if (!params.skip_emptydrops) {
+    if (!params.skip_cellbender) {
         withName: 'CELLBENDER_REMOVEBACKGROUND' {
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}/${meta.id}/cellbender_removebackground" },

diff --git a/conf/test.config b/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'

diff --git a/conf/test_cellranger_multi.config b/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'

diff --git a/docs/output.md b/docs/output.md
@@ -128,7 +128,7 @@ for the corresponding documentation.
 
 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}/cellbender_removebackground`**
 

diff --git a/nextflow.config b/nextflow.config
@@ -50,7 +50,7 @@ params {
     cellrangerarc_reference = null
 
     // Emptydrops parameters
-    skip_emptydrops = false
+    skip_cellbender = false
 
     // CellrangerMulti parameters
     cellranger_vdj_index = null

diff --git a/nextflow_schema.json b/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"
                 }

diff --git a/tests/main_pipeline_cellrangermulti.nf.test b/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
             }
         }
 

diff --git a/tests/nextflow.config b/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'
 }

diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -281,7 +281,7 @@ workflow SCRNASEQ {
     //
     // SUBWORKFLOW: Run cellbender remove background subworkflow
     //
-    if ( !params.skip_emptydrops && !(params.aligner in ['cellrangerarc']) ) {
+    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' }