From 0d5747712df658eeb70c7b0a768f3296cc5cad32 Mon Sep 17 00:00:00 2001 From: Sorel Fitz-Gibbon Date: Thu, 10 Oct 2024 12:57:02 -0700 Subject: [PATCH] add storing of parameters --- CHANGELOG.md | 1 + config/methods.config | 5 +++++ 2 files changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8fd302a3..2ca52a3c 100644 --- 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 index 8d5d3bc7..02f08805 100644 --- 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") + ) } }