4.60. sarscov2_gisaid_ingest

Sanitize data downloaded from GISAID for use in Nextstrain/augur. See: https://nextstrain.github.io/ncov/data-prep#curate-data-from-the-full-gisaid-database

4.60.1. Inputs

4.60.1.1. Required inputs

sarscov2_gisaid_ingest.metadata_gisaid_tsv
File — Default: None
Tab-separated metadata file for sequences downloaded from GISAID and passed in via sequences_gisaid_fasta.

sarscov2_gisaid_ingest.sequences_gisaid_fasta
File — Default: None
Multiple sequences downloaded from GISAID

4.60.1.2. Other inputs

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sarscov2_gisaid_ingest.gcs_out
String? — Default: None
If specified, GCP bucket prefix for storage of the output data.

sarscov2_gisaid_ingest.sanitize_gisaid.disk_size
Int — Default: 750
???

sarscov2_gisaid_ingest.sanitize_gisaid.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???

sarscov2_gisaid_ingest.sanitize_gisaid.nextstrain_ncov_repo_commit
String — Default: "30435fb9ec8de2f045167fb90adfec12f123e80a"
???

sarscov2_gisaid_ingest.sanitize_gisaid.prefix_to_strip
String? — Default: None
String prefix to strip from sequence IDs in both the input fasta and metadata files

4.60.2. Outputs

sarscov2_gisaid_ingest.metadata_gisaid_sanitized_tsv
File
???

sarscov2_gisaid_ingest.sequences_gisaid_sanitized_fasta
File
???


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