418 update cellbender and add gpu support

CHANGELOG.md

@@ -6,6 +6,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## dev
 
 - Add a checker so that `--fb_reference` does not break the pipeline in case `ab` files are not used in `cellranger multi` sub-workflow.
+- Update cellbender module to latest nf-core version
+- Add profile for gpu processes
 
 ## v3.0.0 - 2024-12-09
 

conf/base.config

@@ -50,6 +50,9 @@ process {
     withLabel:process_high_memory {
         memory = { 200.GB * task.attempt }
     }
+    withLabel: process_gpu {
+        ext.use_gpu = { workflow.profile.contains('gpu') }
+    }
     withLabel:error_ignore {
         errorStrategy = 'ignore'
     }

docs/usage.md

@@ -390,6 +390,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
   - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
+- `gpu`
+  - A generic configuration profile for enabling GPU execution for modules that have `process_gpu` label.
 
 ### `-resume`
 

modules.json

@@ -7,7 +7,7 @@
                 "nf-core": {
                     "cellbender/removebackground": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "e01435f46b46adff59546d6a4b4002e31f6c4457",
                         "installed_by": ["modules"]
                     },
                     "cellranger/count": {