feat(cellranger count and multi): Add create-bam option to cellranger count and multi pipelines

CHANGELOG.md

@@ -4,6 +4,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [Unreleased]
+- Add --create-bam parameter to cellranger count and multi pipelines ([#384](https://github.com/nf-core/scrnaseq/issues/384))
 
 ## v2.7.1 - 2024-08-13
 

conf/modules.config

@@ -81,8 +81,8 @@ if(params.aligner == "cellranger") {
                 path: "${params.outdir}/${params.aligner}/count",
                 mode: params.publish_dir_mode
             ]
-            ext.args = {"--chemistry ${meta.chemistry} --create-bam true " + (meta.expected_cells ? "--expect-cells ${meta.expected_cells}" : '')}
-            time   = { 240.h  * task.attempt }
+            ext.args = {"--chemistry ${meta.chemistry} --create-bam ${params.save_align_intermeds}" + " " + (meta.expected_cells ? "--expect-cells ${meta.expected_cells}" : '')}
+            time   = { 240.h * task.attempt }
         }
     }
 }
@@ -185,11 +185,24 @@ if (params.aligner == "star") {
                 enabled: params.save_reference
             ]
         }
-        withName: STAR_ALIGN {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/${meta.id}" },
-                mode: params.publish_dir_mode
-            ]
+
+        if(params.save_align_intermeds) {
+            withName: 'STAR_ALIGN' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/${meta.id}" },
+                    mode: params.publish_dir_mode
+                ]
+            }
+        }
+        else {
+            withName: 'STAR_ALIGN' {
+                publishDir = [
+                    path: { "${params.outdir}/${params.aligner}/${meta.id}" },
+                    mode: params.publish_dir_mode,
+                    pattern: '*',
+                    saveAs: { it.endsWith('.bam') ? null : it }
+                ]
+            }
         }
     }
 }

nextflow.config

@@ -13,6 +13,7 @@ params {
     aligner           = 'alevin'
     input             = null
     save_reference    = false
+    save_align_intermeds = true
     protocol          = 'auto'
 
     // reference files

nextflow_schema.json

@@ -142,6 +142,11 @@
                     "description": "Specify this parameter to save the indices created (STAR, Kallisto, Salmon) to the results.",
                     "fa_icon": "fas fa-bookmark"
                 },
+                "save_align_intermeds": {
+                    "type": "boolean",
+                    "description": "Specify this parameter to save the intermediate alignment files (STAR, CellRanger) to the results.",
+                    "fa_icon": "fas fa-bookmark"
+                },
                 "igenomes_base": {
                     "type": "string",
                     "format": "directory-path",
@@ -551,3 +556,4 @@
         }
     ]
 }
+

workflows/scrnaseq.nf

@@ -242,7 +242,7 @@ workflow SCRNASEQ {
             // add cellranger options that are currently handled by pipeline, coming from samplesheet
             // the module parses them from the 'gex' options
             if (meta.feature_type.toString() == 'gex') {
-                parsed_meta.options['create-bam'] = true  // force bam creation -- param required by cellranger multi
+                parsed_meta.options['create-bam'] = params.save_align_intermeds  // force bam creation -- param required by cellranger multi
                 if (meta.expected_cells) { parsed_meta.options['expected-cells'] = meta.expected_cells }
             }