Add velocyto from bam for cellranger

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fix [#375](https://github.com/nf-core/scrnaseq/issues/375): mismatch between index and probeset when cellranger multi is used without a prebuilt index and an FFPE probeset is passed ([#502](https://github.com/nf-core/scrnaseq/pull/502))
 - Fix [#510](https://github.com/nf-core/scrnaseq/issues/510): Handle files with BOMs. ([#511](https://github.com/nf-core/scrnaseq/pull/511))
 - Address [#512], adding early validation of the cellranger multi barcode sheet ([#513](https://github.com/nf-core/scrnaseq/pull/513))
+- Address [#525], adding velocyto option for the cellranger branch of the pipeline ([#525](https://github.com/nf-core/scrnaseq/pull/525))
 
 ### Chore
 

conf/modules.config

@@ -122,6 +122,19 @@ process {
         time   = { 240.h * task.attempt }
     }
 
+    withName: VELOCYTO {
+        publishDir = [
+            path: "${params.outdir}/${params.aligner}/velocyto",
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> "${meta.id}/${filename}" }
+        ]
+    }
+
+    withName: SAMTOOLS_SORT {
+        ext.prefix = { "cellsorted_${bam.baseName}" }
+        ext.args   = '-t CB -O BAM'
+    }
+
     withName: 'SIMPLEAF_INDEX' {
         publishDir = [
             path: { "${params.outdir}/${params.aligner}" },

modules.json

@@ -85,6 +85,11 @@
                         "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
                         "installed_by": ["modules"]
                     },
+                    "samtools/sort": {
+                        "branch": "master",
+                        "git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7",
+                        "installed_by": ["modules"]
+                    },
                     "simpleaf/index": {
                         "branch": "master",
                         "git_sha": "4ce8f451b1c44e02f5846b39276f5c501ca199ac",
@@ -104,6 +109,11 @@
                         "branch": "master",
                         "git_sha": "b0c3ff2485534c09d9debbf20125d9c6b72ce118",
                         "installed_by": ["modules"]
+                    },
+                    "velocyto": {
+                        "branch": "master",
+                        "git_sha": "ca3514e876459e9dd482a477a281b5b5886a1a84",
+                        "installed_by": ["modules"]
                     }
                 }
             },