Merge pull request #47 from uclahs-cds/nwiltsie_log_params

Use store_object_as_json method to store parameters
uclahs-cds · Dec 22, 2023 · a1be4a8 · a1be4a8
2 parents 9489dfe + bd3485b
commit a1be4a8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Add new flow diagram to README
 - Add additional details to Pipeline Steps section of README
 - Option to provide base recalibration tables for any subset of samples to skip `BaseRecalibrator`
+- Output pipeline parameters to log directory using `store_object_as_json`
 
 ### [Changed]
 - Use modularized `set_env` function

diff --git a/config/methods.config b/config/methods.config
@@ -4,6 +4,7 @@ includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/bam/bam_pa
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/methods/common_methods.config"
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/schema/schema.config"
 includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/retry/retry.config"
+includeConfig "${projectDir}/external/pipeline-Nextflow-config/config/store_object_as_json/store_object_as_json.config"
 
 methods {
 
@@ -129,5 +130,10 @@ methods {
         methods.setup_docker_cpus()
         methods.verify_input_deletion()
         methods.set_recal_tables()
+
+        json_extractor.store_object_as_json(
+            params,
+            new File("${params.log_output_dir}/nextflow-log/params.json")
+        )
     }
 }