4.66. sarscov2_sequencing_reports

Produce per-state and per-collaborator weekly reports of SARS-CoV-2 surveillance data.

4.66.1. Inputs

4.66.1.1. Required inputs

sarscov2_sequencing_reports.assembly_stats_tsvs
Array[File] — Default: None
???

4.66.1.2. Other inputs

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sarscov2_sequencing_reports.max_date
String? — Default: None
???

sarscov2_sequencing_reports.sequencing_report.collab_ids_tsv
File? — Default: None
???

sarscov2_sequencing_reports.sequencing_report.docker
String — Default: "quay.io/broadinstitute/sc2-rmd:0.1.25"
???

sarscov2_sequencing_reports.sequencing_report.intro_blurb
String — Default: "The Broad Institute Viral Genomics group, in partnership with the Genomics Platform and Data Sciences Platform, has been engaged in viral sequencing of COVID-19 patients since March 2020."
???

sarscov2_sequencing_reports.sequencing_report.machine_mem_gb
Int — Default: 7
???

sarscov2_sequencing_reports.sequencing_report.min_date
String? — Default: None
???

sarscov2_sequencing_reports.sequencing_report.min_unambig
Int? — Default: None
???

sarscov2_sequencing_reports.sequencing_report.sequencing_lab
String — Default: "Broad Institute"
???

sarscov2_sequencing_reports.sequencing_report.voc_list
String? — Default: None
???

sarscov2_sequencing_reports.sequencing_report.voi_list
String? — Default: None
???

sarscov2_sequencing_reports.today.timezone
String? — Default: None
???

sarscov2_sequencing_reports.tsv_join.machine_mem_gb
Int — Default: 7
???

sarscov2_sequencing_reports.tsv_join.out_suffix
String — Default: ".txt"
???

4.66.2. Outputs

sarscov2_sequencing_reports.assembly_stats_cumulative_tsv
File
???

sarscov2_sequencing_reports.sequence_report_date
String
???

sarscov2_sequencing_reports.sequencing_report_tsv
File
???

sarscov2_sequencing_reports.sequencing_reports_pdfs
Array[File]
???

sarscov2_sequencing_reports.sequencing_reports_xlsxs
Array[File]
???

sarscov2_sequencing_reports.sequencing_reports_zip
File
???

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