4.46. sarscov2_genbank

Prepare SARS-CoV-2 assemblies for Genbank submission. This includes QC checks with NCBI’s VADR tool and filters out genomes that do not pass its tests.

4.46.1. Inputs

4.46.1.1. Required inputs

sarscov2_genbank.assemblies_fasta
Array[File]+ — Default: None
Genomes to prepare for Genbank submission. One file per genome: all segments/chromosomes included in one file. All fasta files must contain exactly the same number of sequences as reference_fasta (which must equal the number of files in reference_annot_tbl).

sarscov2_genbank.assembly_stats_tsv
File — Default: None
A four column tab text file with one row per sequence and the following header columns: SeqID, Assembly Method, Coverage, Sequencing Technology

sarscov2_genbank.authors_sbt
File — Default: None
A genbank submission template file (SBT) with the author list, created at https://submit.ncbi.nlm.nih.gov/genbank/template/submission/

sarscov2_genbank.biosample_attributes
File — Default: None
A post-submission attributes file from NCBI BioSample, which is available at https://submit.ncbi.nlm.nih.gov/subs/ and clicking on 'Download attributes file with BioSample accessions'.

sarscov2_genbank.passing_package_genbank.account_name
String — Default: None
???

sarscov2_genbank.passing_package_genbank.spuid_namespace
String — Default: None
???

sarscov2_genbank.passing_package_genbank.submission_name
String — Default: None
???

sarscov2_genbank.passing_package_genbank.submission_uid
String — Default: None
???

sarscov2_genbank.weird_package_genbank.account_name
String — Default: None
???

sarscov2_genbank.weird_package_genbank.spuid_namespace
String — Default: None
???

sarscov2_genbank.weird_package_genbank.submission_name
String — Default: None
???

sarscov2_genbank.weird_package_genbank.submission_uid
String — Default: None
???

4.46.1.2. Other inputs

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sarscov2_genbank.assembly_bases.docker
String — Default: "ubuntu"
???

sarscov2_genbank.fasta_rename_map
File? — Default: None
???

sarscov2_genbank.gisaid_prefix
String — Default: 'hCoV-19/'
???

sarscov2_genbank.max_vadr_alerts
Int — Default: 0
???

sarscov2_genbank.min_genome_bases
Int — Default: 15000
???

sarscov2_genbank.passing_gisaid_meta.authors
String? — Default: None
???

sarscov2_genbank.passing_gisaid_meta.continent
String — Default: "North America"
???

sarscov2_genbank.passing_gisaid_meta.originating_lab_addr
String? — Default: None
???

sarscov2_genbank.passing_gisaid_meta.strict
Boolean — Default: true
???

sarscov2_genbank.passing_gisaid_meta.submitting_lab_addr
String? — Default: None
???

sarscov2_genbank.passing_gisaid_meta.submitting_lab_name
String? — Default: None
???

sarscov2_genbank.passing_gisaid_meta.username
String? — Default: None
???

sarscov2_genbank.passing_package_genbank.docker
String — Default: "quay.io/broadinstitute/viral-baseimage:0.1.20"
???

sarscov2_genbank.passing_source_modifiers.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.19.1"
???

sarscov2_genbank.passing_source_modifiers.s_dropout_note
Boolean — Default: true
???

sarscov2_genbank.passing_structured_cmt.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_genbank.rename_fasta_header.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

sarscov2_genbank.rename_fasta_header.out_basename
String — Default: basename(genome_fasta,".fasta")
???

sarscov2_genbank.taxid
Int — Default: 2697049
???

sarscov2_genbank.vadr.docker
String — Default: "staphb/vadr:1.1.3"
???

sarscov2_genbank.vadr.vadr_opts
String — Default: "-s -r --nomisc --mkey NC_045512 --fstlowthr 0.0 --alt_fail lowscore,fsthicnf,fstlocnf,insertnn,deletinn"
???

sarscov2_genbank.weird_gisaid_meta.authors
String? — Default: None
???

sarscov2_genbank.weird_gisaid_meta.continent
String — Default: "North America"
???

sarscov2_genbank.weird_gisaid_meta.originating_lab_addr
String? — Default: None
???

sarscov2_genbank.weird_gisaid_meta.strict
Boolean — Default: true
???

sarscov2_genbank.weird_gisaid_meta.submitting_lab_addr
String? — Default: None
???

sarscov2_genbank.weird_gisaid_meta.submitting_lab_name
String? — Default: None
???

sarscov2_genbank.weird_gisaid_meta.username
String? — Default: None
???

sarscov2_genbank.weird_package_genbank.docker
String — Default: "quay.io/broadinstitute/viral-baseimage:0.1.20"
???

sarscov2_genbank.weird_source_modifiers.docker
String — Default: "quay.io/broadinstitute/viral-phylo:2.1.19.1"
???

sarscov2_genbank.weird_source_modifiers.s_dropout_note
Boolean — Default: true
???

sarscov2_genbank.weird_structured_cmt.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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