Merge pull request #312 from uclahs-cds/sfitz-store-parameters

add storing of parameters
uclahs-cds · Oct 25, 2024 · 0835f91 · 0835f91
2 parents b2ea350 + 0d73ed2
commit 0835f91
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 0 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 ### Added
+- Output pipeline parameters to log directory using `store_object_as_json`
 - Add `panel_of_normals_vcf` for MuTect2.
 - Add `a_mini-all-tools-vcf-input` to `nftest`
 - Add option to input VCFs for intersection

diff --git a/config/methods.config b/config/methods.config
@@ -4,6 +4,7 @@ includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/schema/sch
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/retry/retry.config"
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/methods/common_methods.config"
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/bam/bam_parser.config"
+includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/store_object_as_json/store_object_as_json.config"
 
 methods {
     set_process = {
@@ -152,5 +153,9 @@ methods {
         methods.set_intersect_regions_params()
         methods.set_pipeline_log()
         methods.setup_docker_cpus()
+        json_extractor.store_object_as_json( // must be last
+            params,
+            new File("${params.log_output_dir}/nextflow-log/params.json")
+        )
     }
 }