4.56. sarscov2_biosample_load

Load Broad CRSP metadata and register samples with NCBI BioSample. Return attributes table, id map, etc.

4.56.1. Inputs

4.56.1.1. Required inputs

sarscov2_biosample_load.bioproject
String — Default: None
???

sarscov2_biosample_load.ftp_config_js
File — Default: None
???

sarscov2_biosample_load.id_salt
File — Default: None
???

4.56.1.2. Other inputs

Show/Hide

sarscov2_biosample_load.biosample_submit_tsv
File? — Default: None
???

sarscov2_biosample_load.biosample_submit_tsv_ftp_upload.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.10"
???

sarscov2_biosample_load.biosample_tsv_filter_preexisting.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.10"
???

sarscov2_biosample_load.crsp_meta_etl.allowed_purposes
String — Default: '["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"]'
???

sarscov2_biosample_load.crsp_meta_etl.country
String — Default: 'USA'
???

sarscov2_biosample_load.crsp_meta_etl.docker
String — Default: "quay.io/broadinstitute/py3-bio:0.1.2"
???

sarscov2_biosample_load.crsp_meta_etl.ontology_map_body_part
String — Default: '{"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)", "Other": "Not Provided"}'
???

sarscov2_biosample_load.crsp_meta_etl.ontology_map_states
String — Default: '{"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"}'
???

sarscov2_biosample_load.crsp_meta_etl.org_name_map
String — Default: '{"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"}'
???

sarscov2_biosample_load.crsp_meta_etl.prefix_map
String — Default: '{"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_"}'
???

sarscov2_biosample_load.crsp_meta_etl.sequencing_lab_prefix
String — Default: 'CDCBI'
???

sarscov2_biosample_load.prod_test
String — Default: "Production"
???

sarscov2_biosample_load.sample_meta_crsp
File? — Default: None
???

sarscov2_biosample_load.tsv_join.machine_mem_gb
Int — Default: 7
???

sarscov2_biosample_load.tsv_join.out_suffix
String — Default: ".txt"
???

sarscov2_biosample_load.tsv_join.prefer_first
Boolean — Default: true
???

4.56.2. Outputs

sarscov2_biosample_load.biosample_attributes
File
???

sarscov2_biosample_load.collab_ids_addcols
Array[String]
???

sarscov2_biosample_load.collab_ids_tsv
File?
???

sarscov2_biosample_load.id_map_tsv
File?
???


Generated using WDL AID (1.0.0)