From 5861ced19ad9ef4772f0cc739ba5477f171fde7d Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Sat, 9 Sep 2023 10:34:06 -0400 Subject: [PATCH 1/2] skip two terra-only WDLs on dnax --- pipes/WDL/workflows/terra_table_to_tsv.wdl | 2 ++ pipes/WDL/workflows/terra_update_assemblies.wdl | 2 ++ 2 files changed, 4 insertions(+) diff --git a/pipes/WDL/workflows/terra_table_to_tsv.wdl b/pipes/WDL/workflows/terra_table_to_tsv.wdl index 41987548a..a72ad6284 100644 --- a/pipes/WDL/workflows/terra_table_to_tsv.wdl +++ b/pipes/WDL/workflows/terra_table_to_tsv.wdl @@ -1,5 +1,7 @@ version 1.0 +#DX_SKIP_WORKFLOW + import "../tasks/tasks_terra.wdl" as terra workflow terra_table_to_tsv { diff --git a/pipes/WDL/workflows/terra_update_assemblies.wdl b/pipes/WDL/workflows/terra_update_assemblies.wdl index b81b266ed..4ac69137b 100644 --- a/pipes/WDL/workflows/terra_update_assemblies.wdl +++ b/pipes/WDL/workflows/terra_update_assemblies.wdl @@ -1,5 +1,7 @@ version 1.0 +#DX_SKIP_WORKFLOW + import "../tasks/tasks_terra.wdl" as terra workflow update_data_tables { From b3f05f87729210c489cf64ebda70fb5b739b8c0b Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Sat, 9 Sep 2023 10:39:10 -0400 Subject: [PATCH 2/2] yaml.load without loader deprecated, switch to safe_load --- pipes/dnax/dx-launcher/dx-yml-build | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/dnax/dx-launcher/dx-yml-build b/pipes/dnax/dx-launcher/dx-yml-build index 737329280..29d001d96 100755 --- a/pipes/dnax/dx-launcher/dx-yml-build +++ b/pipes/dnax/dx-launcher/dx-yml-build @@ -14,7 +14,7 @@ app_basename=os.path.splitext(os.path.basename(app_yaml_path))[0] output_json_filename=app_basename+'.json' with open(app_yaml_path) as infile: - data = yaml.load(infile) + data = yaml.safe_load(infile) data["00COMMENT"] = "This {}.json has been generated from {} automatically using dx-yml-build".format(app_basename,app_yaml_path) with open(output_json_filename, 'w') as outfile: json.dump(data, outfile, sort_keys=True, indent=2)