From 51db1d58d6e694a6fa166be311bc7a82f028c8ed Mon Sep 17 00:00:00 2001 From: Danny Park Date: Sat, 25 Sep 2021 20:33:48 -0400 Subject: [PATCH] update org names --- pipes/WDL/tasks/tasks_sarscov2.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pipes/WDL/tasks/tasks_sarscov2.wdl b/pipes/WDL/tasks/tasks_sarscov2.wdl index 8dc23f1d6..c3059c6a0 100644 --- a/pipes/WDL/tasks/tasks_sarscov2.wdl +++ b/pipes/WDL/tasks/tasks_sarscov2.wdl @@ -402,8 +402,8 @@ task crsp_meta_etl { String country = 'USA' String ontology_map_states = '{"AL": "Alabama", "AK": "Alaska", "AZ": "Arizona", "AR": "Arkansas", "CA": "California", "CO": "Colorado", "CT": "Connecticut", "DE": "Delaware", "DC": "District of Columbia", "FL": "Florida", "GA": "Georgia", "HI": "Hawaii", "ID": "Idaho", "IL": "Illinois", "IN": "Indiana", "IA": "Iowa", "KS": "Kansas", "KY": "Kentucky", "LA": "Louisiana", "ME": "Maine", "MD": "Maryland", "MA": "Massachusetts", "MI": "Michigan", "MN": "Minnesota", "MS": "Mississippi", "MO": "Missouri", "MT": "Montana", "NE": "Nebraska", "NV": "Nevada", "NH": "New Hampshire", "NJ": "New Jersey", "NM": "New Mexico", "NY": "New York", "NC": "North Carolina", "ND": "North Dakota", "OH": "Ohio", "OK": "Oklahoma", "OR": "Oregon", "PA": "Pennsylvania", "RI": "Rhode Island", "SC": "South Carolina", "SD": "South Dakota", "TN": "Tennessee", "TX": "Texas", "UT": "Utah", "VT": "Vermont", "VA": "Virginia", "WA": "Washington", "WV": "West Virginia", "WI": "Wisconsin", "WY": "Wyoming"}' String ontology_map_body_part = '{"AN SWAB": "Anterior Nares", "AN Swab": "Anterior Nares", "Anterior Nares": "Anterior Nares", "Swab": "Upper respiratory tract", "Viral": "Upper respiratory tract", "Null": "Anterior Nares", "NP Swab": "Nasopharynx (NP)", "Nasopharynx (NP)": "Nasopharynx (NP)", "Oropharynx (OP)": "Oropharynx (OP)"}' - String prefix_map = '{"Broad Institute Clinical Research Sequencing Platform": "CRSP_", "Massachusetts General Hospital": "MGH_", "Rhode Island Department of Health": "RIDOH_", "Biobot Analytics": "Biobot_"}' - String org_name_map = '{"Broad Institute Clinical Research Sequencing Platform": "Broad Institute Clinical Research Sequencing Platform", "Massachusetts General Hospital": "Massachusetts General Hospital", "RIDOH": "Rhode Island Department of Health", "Biobot Analytics": "Biobot Analytics"}' + String prefix_map = '{"Broad Institute Clinical Research Sequencing Platform": "CRSP_", "Massachusetts General Hospital": "MGH_", "Rhode Island Department of Health": "RIDOH_", "Biobot Analytics": "Biobot_", "Flow Health":"FlowHealth_", "Colorado Mesa University":"CMU_", "Capture Diagnostics Hawaii":"Capture_", "Boston Medical Center":"BMC_", "University of Central Florida":"UCF_"}' + String org_name_map = '{"Broad Institute Clinical Research Sequencing Platform": "Broad Institute Clinical Research Sequencing Platform", "Massachusetts General Hospital": "Massachusetts General Hospital", "RIDOH": "Rhode Island Department of Health", "BIOBOT": "Biobot Analytics", "FLOW":"Flow Health", "MESA":"Colorado Mesa University", "CAPTURE":"Capture Diagnostics Hawaii", "BUBMC":"Boston Medical Center", "UCF":"University of Central Florida"}' String allowed_purposes = '["Baseline surveillance (random sampling)", "Targeted surveillance (non-random sampling)", "Screening for Variants of Concern (VOC)", "Longitudinal surveillance (repeat sampling of individuals)", "Vaccine escape surveillance", "Cluster/Outbreak investigation"]' String docker = "quay.io/broadinstitute/py3-bio:0.1.2"