Troubleshootin t1dgrs2 pipeline

RTIInternational · Apr 28, 2024 · 99c40d8 · 99c40d8
1 parent 89010fb
commit 99c40d8
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 9 deletions.
diff --git a/t1dgrs2_pipeline/v1.0/t1dgrs2_pipeline.json b/t1dgrs2_pipeline/v1.0/t1dgrs2_pipeline.json
@@ -99,7 +99,8 @@
                         "consented_gvcfs_dir": "<inputs.output_dir>/gvcfs_consented/",
                         "nonconsented_gvcfs_dir": "<inputs.output_dir>/gvcfs_nonconsented/",
                         "master_rti_manifest": "<inputs.master_rti_manifest>",
-                        "new_rti_manifest": "<inputs.new_rti_manifest>"
+                        "new_rti_manifest": "<inputs.new_rti_manifest>",
+                        "genedx_manifest_path": "<steps.download_gvcfs_from_s3.outputs.genedx_manifest_path>"
                     }
                 },
                 "returncode_1": { 
@@ -115,6 +116,7 @@
                     "inputs": {
                         "gvcf_dir": "<inputs.output_dir>/gvcfs_consented/",
                         "variant_list": "<inputs.variant_list>",
+                        "genedx_manifest": "<steps.filter_gvcfs_by_consent.outputs.genedx_manifest>",
                         "out_dir": "<inputs.output_dir>/t1dgrs/",
                         "working_dir": "<inputs.working_dir>/batch_calculate_t1dgrs2/",
                         "argo_api_url": "<inputs.argo_api_url>",

diff --git a/t1dgrs2_pipeline/v1.0/t1dgrs2_tasks.json b/t1dgrs2_pipeline/v1.0/t1dgrs2_tasks.json
@@ -41,9 +41,9 @@
                 "type": "file",
                 "value": "<inputs.downloaded_samples>"
             },
-            "gene_dx_manifest_path": {
+            "genedx_manifest_path": {
                 "type": "file",
-                "value": "<inputs.target_dir>/gene_dx_manifest_path.txt"
+                "value": "<inputs.target_dir>/genedx_manifest_path.txt"
             },
             "log": {
                 "type": "file",
@@ -71,7 +71,7 @@
             "new_rti_manifest": {
                 "type": "file"
             },
-            "gene_dx_manifest_path": {
+            "genedx_manifest_path": {
                 "type": "file"
             }
         },
@@ -89,8 +89,8 @@
             "<inputs.master_rti_manifest>",
             "--new_rti_manifest",
             "<inputs.new_rti_manifest>",
-            "--gene_dx_manifest_path",
-            "<inputs.gene_dx_manifest_path>"
+            "--genedx_manifest_path",
+            "<inputs.genedx_manifest_path>"
         ],
         "outputs": {
             "genedx_manifest": {
@@ -111,7 +111,7 @@
             "variant_list": {
                 "type": "file"
             },
-            "gene_dx_manifest_path": {
+            "genedx_manifest": {
                 "type": "file"
             },
             "out_dir": {
@@ -140,8 +140,8 @@
             "<inputs.gvcf_dir>",
             "--variant_list",
             "<inputs.variant_list>",
-            "--gene_dx_manifest_path",
-            "<inputs.gene_dx_manifest_path>",
+            "--genedx_manifest",
+            "<inputs.genedx_manifest>",
             "--out_dir",
             "<inputs.out_dir>",
             "--working_dir",