4.58. 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.
4.58.1. Inputs¶
4.58.1.1. 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.author_sbt_defaults_yaml
File — Default: None
A YAML file with default values to use for the submitter, submitter affiliation, and author affiliation. Optionally including authors at the start and end of the author_list. Example: gs://pathogen-public-dbs/other-related/default_sbt_values.yaml
sarscov2_genbank.author_sbt_j2_template
File — Default: None
A jinja2-format template for the sbt file expected by NCBI. Example: gs://pathogen-public-dbs/other-related/author_template.sbt.j2
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_gisaid_meta.submitting_lab_name
String — Default: None
???
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_gisaid_meta.submitting_lab_name
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
???
4.58.1.2. Other inputs¶
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sarscov2_genbank.assembly_bases.docker
String — Default: "ubuntu"
???
sarscov2_genbank.author_list
String? — Default: None
A string containing a space-delimited list with of author surnames separated by first name and (optional) middle initial. Ex. 'Lastname,Firstname, Last-hypenated,First,M., Last,F.'
sarscov2_genbank.fasta_rename_map
File? — Default: None
???
sarscov2_genbank.generate_author_sbt.docker
String — Default: "quay.io/broadinstitute/py3-bio:0.1.2"
???
sarscov2_genbank.generate_author_sbt.out_base
String? — Default: "authors"
prefix to use for the generated *.sbt output file
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_fasta.cpus
Int — Default: 4
???
sarscov2_genbank.passing_gisaid_meta.address_map
String — Default: '{}'
???
sarscov2_genbank.passing_gisaid_meta.authors_map
String — Default: '{}'
???
sarscov2_genbank.passing_gisaid_meta.continent
String — Default: "North America"
???
sarscov2_genbank.passing_gisaid_meta.strict
Boolean — Default: true
???
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:2.1.20.2"
???
sarscov2_genbank.passing_source_modifiers.s_dropout_note
Boolean — Default: true
???
sarscov2_genbank.passing_structured_cmt.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_genbank.rename_fasta_header.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_genbank.rename_fasta_header.out_basename
String — Default: basename(genome_fasta,".fasta")
???
sarscov2_genbank.taxid
Int — Default: 2697049
???
sarscov2_genbank.vadr.cpus
Int — Default: 2
???
sarscov2_genbank.vadr.docker
String — Default: "quay.io/staphb/vadr:1.5.1"
???
sarscov2_genbank.vadr.maxlen
Int — Default: 30000
???
sarscov2_genbank.vadr.mem_size
Int — Default: 4
???
sarscov2_genbank.vadr.minlen
Int — Default: 50
???
sarscov2_genbank.vadr.vadr_opts
String — Default: "--glsearch -s -r --nomisc --mkey sarscov2 --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn"
???
sarscov2_genbank.weird_fasta.cpus
Int — Default: 4
???
sarscov2_genbank.weird_gisaid_meta.address_map
String — Default: '{}'
???
sarscov2_genbank.weird_gisaid_meta.authors_map
String — Default: '{}'
???
sarscov2_genbank.weird_gisaid_meta.continent
String — Default: "North America"
???
sarscov2_genbank.weird_gisaid_meta.strict
Boolean — Default: true
???
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:2.1.20.2"
???
sarscov2_genbank.weird_source_modifiers.s_dropout_note
Boolean — Default: true
???
sarscov2_genbank.weird_structured_cmt.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
4.58.2. Outputs¶
sarscov2_genbank.gisaid_fasta
File
???
sarscov2_genbank.gisaid_meta_csv
File
???
sarscov2_genbank.num_input
Int
???
sarscov2_genbank.num_successful
Int
???
sarscov2_genbank.num_weird
Int
???
sarscov2_genbank.submission_xml
File
???
sarscov2_genbank.submission_zip
File
???
sarscov2_genbank.submit_ready
File
???
sarscov2_genbank.vadr_outputs
Array[File]
???
sarscov2_genbank.weird_genbank_xml
File
???
sarscov2_genbank.weird_genbank_zip
File
???
sarscov2_genbank.weird_gisaid_fasta
File
???
sarscov2_genbank.weird_gisaid_meta_csv
File
???
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