Added hla and non-hla variant list parameters to pipeline config for …

…batch_extract_gvcf_variants
RTIInternational · Sep 23, 2024 · 4349137 · 4349137
1 parent bcdf34c
commit 4349137
Show file tree

Hide file tree

Showing 2 changed files with 12 additions and 0 deletions.
diff --git a/t1dgrs2_pipeline/v2.0/pipeline_config/entrypoint_download.json b/t1dgrs2_pipeline/v2.0/pipeline_config/entrypoint_download.json
@@ -107,6 +107,8 @@
                         "output_dir": "<inputs.output_dir>batch_extract_gvcf_variants",
                         "gvcf_dir": "<inputs.output_dir>download_gvcfs_from_revvity_sftp/gvcfs",
                         "variant_list": "/pipeline/inputs/t1dgrs2_hg19_variants_<inputs.variant_list_version>.tsv",
+                        "hla_variants_file": "/pipeline/inputs/hla_variants_<inputs.variant_list_version>.txt",
+                        "non_hla_variants_file": "/pipeline/inputs/non_hla_variants_<inputs.variant_list_version>.txt",
                         "argo_api_url": "<inputs.argo_api_url>",
                         "simultaneous_jobs": "<inputs.simultaneous_jobs>"
                     }

diff --git a/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json b/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json
@@ -79,6 +79,12 @@
             "variant_list": {
                 "type": "file"
             },
+            "hla_variants_file": {
+                "type": "file"
+            },
+            "non_hla_variants_file": {
+                "type": "file"
+            },
             "argo_api_url": {
                 "type": "str",
                 "default": "http://argo-early-check-rs-1-server:2746/api/v1/workflows/early-check-rs-1"
@@ -99,6 +105,10 @@
             "<inputs.gvcf_dir>",
             "--variant_list",
             "<inputs.variant_list>",
+            "--hla_variants_file",
+            "<inputs.hla_variants_file>",
+            "--non_hla_variants_file",
+            "<inputs.non_hla_variants_file>",
             "--argo_api_url",
             "<inputs.argo_api_url>",
             "--simultaneous_jobs",