Fix for STAR chemistry issue #60

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixes
 
 - Make sure pipeline runs on multiple samples [#77](https://github.com/nf-core/scrnaseq/pull/77)
+- Fix issue where STARsolo always uses 10XV2 chemistry [#60](https://github.com/nf-core/scrnaseq/issues/60)
 
 ## v1.1.0 - 2021-03-24 "Olive Mercury Corgi"
 

lib/WorkflowScrnaseq.groovy

@@ -77,6 +77,7 @@ class WorkflowScrnaseq {
     static formatProtocol(protocol, aligner) {
         String new_protocol = protocol
         String chemistry = ''
+        String other_parameters = ''
 
         // alevin
         if (aligner == 'alevin') {
@@ -104,14 +105,17 @@ class WorkflowScrnaseq {
                 case '10XV1':
                     new_protocol = 'CB_UMI_Simple'
                     chemistry = 'V1'
+                    other_parameters = '--soloUMIlen 10'
                     break
                 case '10XV2':
                     new_protocol = 'CB_UMI_Simple'
                     chemistry = 'V2'
+                    other_parameters = '--soloUMIlen 10'
                     break
                 case '10XV3':
                     new_protocol = 'CB_UMI_Simple'
                     chemistry = 'V3'
+                    other_parameters = '--soloUMIlen 12'
                     break
                 case 'dropseq':
                     new_protocol = 'CB_UMI_Simple'
@@ -147,7 +151,7 @@ class WorkflowScrnaseq {
             exit 1, 'Aligner not recognized.'
         }
 
-        return [new_protocol, chemistry]
+        return [new_protocol, chemistry, other_parameters]
     }
 
 }

modules/local/star_align.nf

@@ -17,6 +17,7 @@ process STAR_ALIGN {
     path  gtf
     path whitelist
     val protocol
+    val other_10x_parameters
 
     output:
     tuple val(meta), path('*d.out.bam')       , emit: bam
@@ -50,6 +51,7 @@ process STAR_ALIGN {
         --outFileNamePrefix $prefix. \\
         --soloCBwhitelist <(gzip -cdf $whitelist) \\
         --soloType $protocol \\
+        $other_10x_parameters \\
         $out_sam_type \\
         $ignore_gtf \\
         $seq_center \\

subworkflows/local/starsolo.nf

@@ -16,6 +16,7 @@ workflow STARSOLO {
     protocol
     barcode_whitelist
     ch_fastq
+    other_10x_parameters
 
     main:
     ch_versions = Channel.empty()
@@ -42,7 +43,8 @@ workflow STARSOLO {
         star_index,
         gtf,
         barcode_whitelist,
-        protocol
+        protocol,
+        other_10x_parameters
     )
     ch_versions = ch_versions.mix(STAR_ALIGN.out.versions)
 

workflows/scrnaseq.nf

@@ -63,7 +63,7 @@ include { MULTIQC } from "../modules/local/multiqc"
 // TODO: Are this channels still necessary?
 ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
 ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
-(protocol, chemistry) = WorkflowScrnaseq.formatProtocol(params.protocol, params.aligner)
+(protocol, chemistry, other_parameters) = WorkflowScrnaseq.formatProtocol(params.protocol, params.aligner)
 
 // general input and params
 ch_input = file(params.input)
@@ -145,7 +145,8 @@ workflow SCRNASEQ {
             ch_star_index,
             protocol,
             ch_barcode_whitelist,
-            ch_fastq
+            ch_fastq,
+            other_parameters
         )
         ch_versions = ch_versions.mix(STARSOLO.out.ch_versions)
         ch_multiqc_star = STARSOLO.out.for_multiqc