Merge pull request #317 from nf-core/316-update-cellranger-modules-to…

…-latest-nf-coremodules-versions 316 update cellranger modules to latest nf coremodules versions
nf-core · Apr 16, 2024 · 7c15e0a · 7c15e0a
2 parents 1043441 + 984c101
commit 7c15e0a
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Showing 24 changed files with 356 additions and 114 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Update to kallisto|bustools v0.28.2 ([#294](https://github.com/nf-core/scrnaseq/pull/294))
 - Fix cellrangerarc matrix conversions and protocol selection ([#300](https://github.com/nf-core/scrnaseq/pull/300))
 - Add new emptydrops calling module ([#301](https://github.com/nf-core/scrnaseq/pull/301))
+- Update cellranger modules to latest version ([[#316](https://github.com/nf-core/scrnaseq/issues/316)])
 
 ## v2.5.1
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -98,7 +98,7 @@ if(params.aligner == "cellranger") {
                 path: "${params.outdir}/${params.aligner}/count",
                 mode: params.publish_dir_mode
             ]
-            ext.args = {"--chemistry ${meta.chemistry} " + (meta.expected_cells ? "--expect-cells ${meta.expected_cells}" : '')}
+            ext.args = {"--chemistry ${meta.chemistry} --create-bam true " + (meta.expected_cells ? "--expect-cells ${meta.expected_cells}" : '')}
             time   = { check_max( 240.h  * task.attempt, 'time'    ) }
         }
     }

diff --git a/modules.json b/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "cellranger/count": {
                         "branch": "master",
-                        "git_sha": "92ca535c5a8c0fe89eb71e649ee536bd355ce4fc",
+                        "git_sha": "e66183d2ab6a5c2f3fd66b2bee942287cf65536c",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkgtf": {
                         "branch": "master",
-                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
+                        "git_sha": "e66183d2ab6a5c2f3fd66b2bee942287cf65536c",
                         "installed_by": ["modules"]
                     },
                     "cellranger/mkref": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "e66183d2ab6a5c2f3fd66b2bee942287cf65536c",
                         "installed_by": ["modules"]
                     },
                     "cellrangerarc/count": {

diff --git a/modules/nf-core/cellranger/count/main.nf b/modules/nf-core/cellranger/count/main.nf
diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml
diff --git a/modules/nf-core/cellranger/count/tests/main.nf.test b/modules/nf-core/cellranger/count/tests/main.nf.test
diff --git a/modules/nf-core/cellranger/count/tests/main.nf.test.snap b/modules/nf-core/cellranger/count/tests/main.nf.test.snap
diff --git a/modules/nf-core/cellranger/count/tests/nextflow.config b/modules/nf-core/cellranger/count/tests/nextflow.config
diff --git a/modules/nf-core/cellranger/mkgtf/environment.yml b/modules/nf-core/cellranger/mkgtf/environment.yml
diff --git a/modules/nf-core/cellranger/mkgtf/main.nf b/modules/nf-core/cellranger/mkgtf/main.nf
diff --git a/modules/nf-core/cellranger/mkgtf/meta.yml b/modules/nf-core/cellranger/mkgtf/meta.yml
diff --git a/modules/nf-core/cellranger/mkgtf/tests/main.nf.test b/modules/nf-core/cellranger/mkgtf/tests/main.nf.test