Fixing issue #297

nf-core · Feb 2, 2024 · 59648cc · 59648cc
1 parent ddf3e1d
commit 59648cc
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git a/assets/protocols.json b/assets/protocols.json
@@ -30,6 +30,11 @@
             "protocol": "SC3Pv3"
         }
     },
+    "cellrangerarc": {
+        "auto": {
+            "protocol": "auto"
+        }
+    },
     "star": {
         "10XV1": {
             "protocol": "CB_UMI_Simple",

diff --git a/workflows/scrnaseq.nf b/workflows/scrnaseq.nf
@@ -71,7 +71,7 @@ include { MULTIQC                     } from '../modules/nf-core/multiqc/main'
 ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
 ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
 protocol_config = WorkflowScrnaseq.getProtocol(workflow, log, params.aligner, params.protocol)
-if (protocol_config['protocol'] == 'auto' && params.aligner != "cellranger") {
+if (protocol_config['protocol'] == 'auto' && ( params.aligner != "cellranger" && params.aligner != "cellrangerarc") ) {
     error "Only cellranger supports `protocol = 'auto'`. Please specify the protocol manually!"
 }