4.55. sarscov2_batch_relineage

Re-call Nextclade and Pangolin lineages on a flowcell’s worth of SARS-CoV-2 genomes

4.55.1. Inputs

4.55.1.1. Required inputs

sarscov2_batch_relineage.flowcell_id
String — Default: None
???

sarscov2_batch_relineage.genomes_fasta
Array[File] — Default: None
???

sarscov2_batch_relineage.metadata_annotated_tsv
File — Default: None
???

sarscov2_batch_relineage.metadata_raw_tsv
File — Default: None
???

4.55.1.2. Other inputs

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sarscov2_batch_relineage.filter_sequences_by_length.disk_size
Int — Default: 750
???

sarscov2_batch_relineage.filter_sequences_by_length.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

sarscov2_batch_relineage.merge_annotated.machine_mem_gb
Int — Default: 7
???

sarscov2_batch_relineage.merge_annotated.prefer_first
Boolean — Default: true
???

sarscov2_batch_relineage.merge_raw.machine_mem_gb
Int — Default: 7
???

sarscov2_batch_relineage.merge_raw.prefer_first
Boolean — Default: true
???

sarscov2_batch_relineage.min_genome_bases
Int — Default: 24000
???

sarscov2_batch_relineage.nextclade_many_samples.auspice_reference_tree_json
File? — Default: None
???

sarscov2_batch_relineage.nextclade_many_samples.disk_size
Int — Default: 150
???

sarscov2_batch_relineage.nextclade_many_samples.docker
String — Default: "nextstrain/nextclade:2.12.0"
???

sarscov2_batch_relineage.nextclade_many_samples.gene_annotations_json
File? — Default: None
???

sarscov2_batch_relineage.nextclade_many_samples.pcr_primers_csv
File? — Default: None
???

sarscov2_batch_relineage.nextclade_many_samples.qc_config_json
File? — Default: None
???

sarscov2_batch_relineage.nextclade_many_samples.root_sequence
File? — Default: None
???

sarscov2_batch_relineage.nextclade_many_samples.virus_properties
File? — Default: None
???

sarscov2_batch_relineage.pangolin_many_samples.analysis_mode
String? — Default: None
???

sarscov2_batch_relineage.pangolin_many_samples.docker
String — Default: "quay.io/staphb/pangolin:4.3.1-pdata-1.22"
???

sarscov2_batch_relineage.pangolin_many_samples.max_ambig
Float? — Default: None
???

sarscov2_batch_relineage.pangolin_many_samples.min_length
Int? — Default: None
???

sarscov2_batch_relineage.pangolin_many_samples.update_dbs_now
Boolean — Default: false
???

sarscov2_batch_relineage.today.timezone
String? — Default: None
???

4.55.2. Outputs

sarscov2_batch_relineage.assembly_stats_final_relineage_tsv
File
???

sarscov2_batch_relineage.assembly_stats_relineage_tsv
File
???

sarscov2_batch_relineage.nextalign_msa
File
???

sarscov2_batch_relineage.nextclade_all_json
File
???

sarscov2_batch_relineage.nextclade_all_tsv
File
???

sarscov2_batch_relineage.nextclade_auspice_json
File
???

sarscov2_batch_relineage.pangolin_msa
File
???

sarscov2_batch_relineage.pangolin_report
File
???

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