From 3cbd825466d8d0f534ce765971dd8452da94b66d Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Thu, 25 Jul 2024 09:40:22 -0700 Subject: [PATCH] Add WDL and json file for writing both inventories --- primed_inventories.json | 9 +++++++++ primed_inventories.wdl | 31 +++++++++++++++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 primed_inventories.json create mode 100644 primed_inventories.wdl diff --git a/primed_inventories.json b/primed_inventories.json new file mode 100644 index 0000000..03780d0 --- /dev/null +++ b/primed_inventories.json @@ -0,0 +1,9 @@ +{ + "primed_inventories.workspaces": { + "primed-data-prevent-1/PRIMED_ARIC_DBGAP_PHS000280_V8_P2_HMB-IRB": "ARIC", + "primed-data-dprism-1/PRIMED_RPGEH_DBGAP_PHS000788_V2_P3_HMB-IRB-NPU": "GERA, RPGEH", + "primed-data-topmed-1/PRIMED_CARDIA_TOPMED_DBGAP_PHS001612_V1_P1_HMB-IRB": "CARDIA" + }, + "primed_inventories.output_workspace_namespace": "primed-adrienne", + "primed_inventories.output_workspace_name": "primed-sandbox" +} diff --git a/primed_inventories.wdl b/primed_inventories.wdl new file mode 100644 index 0000000..3932e3c --- /dev/null +++ b/primed_inventories.wdl @@ -0,0 +1,31 @@ +version 1.0 + +import "primed_phenotype_inventory.wdl" as phenotype_inventory +import "primed_genotype_inventory.wdl" as genotype_inventory + +workflow primed_inventories { + input { + Map[String, String] workspaces + String output_workspace_name + String output_workspace_namespace + } + + call phenotype_inventory.write_primed_phenotype_inventory_table { + input: workspaces = workspaces, + output_workspace_name = output_workspace_name, + output_workspace_namespace = output_workspace_namespace, + output_table = "phenotype_inventory" + } + + call genotype_inventory.write_primed_genotype_inventory_table { + input: workspaces = workspaces, + output_workspace_name = output_workspace_name, + output_workspace_namespace = output_workspace_namespace, + output_table = "genotype_inventory" + } + + meta { + author: "Adrienne stilp" + email: "amstilp@uw.edu" + } +}