Merge pull request #27 from uclahs-cds/yashpatel-parameterize-deletio…

…n-by-state

Deletion state parameterization

CHANGELOG.md

@@ -11,6 +11,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
+## [1.0.0-rc.3] - 2023-08-09
+### [Added]
+- Customization options for which input BAMs to delete with metapipeline
+
+---
+
 ## [1.0.0-rc.2] - 2023-08-02
 ### [Added]
 - Custom resource allocation updates through configuration parameters

README.md

@@ -130,7 +130,8 @@ For normal-only or tumour-only samples, exclude the fields for the other state.
 | `work_dir` | optional | path | Path of working directory for Nextflow. When included in the sample config file, Nextflow intermediate files and logs will be saved to this directory. With ucla_cds, the default is `/scratch` and should only be changed for testing/development. Changing this directory to `/hot` or `/tmp` can lead to high server latency and potential disk space limitations, respectively. |
 | `docker_container_registry` | optional | string | Registry containing tool Docker images. Default: `ghcr.io/uclahs-cds` |
 | `metapipeline_delete_input_bams` | optional | boolean | Set to true to delete the input BAM files once the initial processing step is complete. **WARNING**: This option should NOT be used for individual runs of call-gSNP; it's intended for metapipeline-DNA to optimize disk space usage by removing files that are no longer needed from the `workDir`. |
-| `metapipeline_final_output_dir` | optional | string | Absolute path for the final output directory of metapipeline-DNA that's expected to contain the output BAM from align-DNA. **WARNING**: This option should not be used for individual runs of call-gSNP; it's intended for metapipeline-DNA to optimize disk space usage. |
+| `metapipeline_final_output_dir` | optional | string | Absolute path for the final output directory of metapipeline-DNA that's expected to contain the output BAM from align-DNA. **WARNING**: This option should not be used for individual runs of recalibrate-BAM; it's intended for metapipeline-DNA to optimize disk space usage. |
+| `metapipeline_states_to_delete` | optional | list | List of states for which to delete input BAMs. **WARNING**: This option should not be used for individual runs of recalibrate-BAM; it's intended for metapipeline-DNA to optimize disk space usage. |
 | `base_resource_update` | optional | namespace | Namespace of parameters to update base resource allocations in the pipeline. Usage and structure are detailed in `template.config` and below. |
 
 #### Base resource allocation updaters

config/default.config

@@ -14,6 +14,7 @@ params {
     cache_intermediate_pipeline_steps = false
 
     metapipeline_delete_input_bams = false
+    metapipeline_states_to_delete = ['normal', 'tumor']
 
     docker_container_registry = "ghcr.io/uclahs-cds"
 

config/schema.yaml

@@ -85,6 +85,16 @@ metapipeline_final_output_dir:
   type: 'String'
   required: false
   help: 'Directory containing final outputs to check before input deletion'
+metapipeline_states_to_delete:
+  type: 'List'
+  required: true
+  help: 'List of states for which to delete input BAMs'
+  default:
+    - 'normal'
+    - 'tumor'
+  choice:
+    - 'normal'
+    - 'tumor'
 base_resource_update:
   type: 'ResourceUpdateNamespace'
   required: false

main.nf

@@ -153,6 +153,7 @@ workflow {
     *   Input file deletion
     */
     input_ch_samples_with_index
+        .filter{ params.metapipeline_states_to_delete.contains(it.sample_type) }
         .map{ sample -> sample.path }
         .flatten()
         .unique()

nextflow.config

@@ -3,5 +3,5 @@ manifest {
     name = 'recalibrate-BAM'
     author = 'Yash Patel'
     description = 'Nextflow pipeline to perform Indel Realignment and Base Quality Score Recalibration'
-    version = '1.0.0-rc.2'
+    version = '1.0.0-rc.3'
 }