4.57. sarscov2_data_release

Submit data bundles to databases and repositories

4.57.1. Inputs

4.57.1.1. Required inputs

sarscov2_data_release.cdc_aligned_trimmed_bams
Array[File] — Default: None
???

sarscov2_data_release.flowcell_id
String — Default: None
???

sarscov2_data_release.genbank_xml
File — Default: None
???

sarscov2_data_release.genbank_zip
File — Default: None
???

sarscov2_data_release.sra_bioproject
String — Default: None
???

sarscov2_data_release.sra_data_bucket_uri
String — Default: None
???

sarscov2_data_release.sra_meta_tsv
File — Default: None
???

4.57.1.2. Other inputs

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sarscov2_data_release.cdc_cumulative_metadata
File? — Default: None
???

sarscov2_data_release.cdc_final_metadata
File? — Default: None
???

sarscov2_data_release.cdc_passing_fasta
File? — Default: None
???

sarscov2_data_release.cdc_s3_credentials
File? — Default: None
???

sarscov2_data_release.cdc_s3_uri
String? — Default: None
???

sarscov2_data_release.dashboard_bucket_uri
String? — Default: None
???

sarscov2_data_release.ftp_path_prefix
String — Default: basename(genbank_zip,".zip")
???

sarscov2_data_release.gcs_out_reporting
String? — Default: None
???

sarscov2_data_release.genbank_upload.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.10"
???

sarscov2_data_release.gisaid_auth_token
File? — Default: None
???

sarscov2_data_release.gisaid_csv
File? — Default: None
???

sarscov2_data_release.gisaid_fasta
File? — Default: None
???

sarscov2_data_release.gisaid_uploader.database
String — Default: "EpiCoV"
???

sarscov2_data_release.gisaid_uploader.frameshift
String — Default: "catch_novel"
???

sarscov2_data_release.meta_final_csv.out_basename
String — Default: basename(basename(tsv,'.tsv'),'.txt')
???

sarscov2_data_release.meta_sanitize.docker
String — Default: "quay.io/broadinstitute/py3-bio:0.1.2"
???

sarscov2_data_release.ncbi_ftp_config_js
File? — Default: None
???

sarscov2_data_release.prod_test
String — Default: "Production"
???

sarscov2_data_release.s3_cdc_complete.cpus
Int — Default: 2
???

sarscov2_data_release.s3_cdc_complete.disk_gb
Int — Default: 1000
???

sarscov2_data_release.s3_cdc_dump_cumulative.cpus
Int — Default: 2
???

sarscov2_data_release.s3_cdc_dump_cumulative.disk_gb
Int — Default: 1000
???

sarscov2_data_release.s3_cdc_dump_cumulative.nop_block
String? — Default: None
???

sarscov2_data_release.s3_cdc_dump_meta.cpus
Int — Default: 2
???

sarscov2_data_release.s3_cdc_dump_meta.disk_gb
Int — Default: 1000
???

sarscov2_data_release.s3_cdc_dump_meta.nop_block
String? — Default: None
???

sarscov2_data_release.s3_cdc_dump_reads.nop_block
String? — Default: None
???

sarscov2_data_release.sra_tsv_to_xml.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.10"
???

sarscov2_data_release.sra_upload.docker
String — Default: "quay.io/broadinstitute/ncbi-tools:2.10.7.10"
???

4.57.2. Outputs

sarscov2_data_release.genbank_response
Array[File]
???

sarscov2_data_release.sra_response
Array[File]
???

sarscov2_data_release.sra_xml
File?
???

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