4.65. sarscov2_nextstrain_aligned_input¶
Take aligned assemblies, build trees, and convert to json representation suitable for Nextstrain visualization. See https://nextstrain.org/docs/getting-started/ and https://nextstrain-augur.readthedocs.io/en/stable/
4.65.1. Inputs¶
4.65.1.1. Required inputs¶
sarscov2_nextstrain_aligned_input.build_name
String — Default: None
???
sarscov2_nextstrain_aligned_input.builds_yaml
File — Default: None
???
4.65.1.2. Other inputs¶
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sarscov2_nextstrain_aligned_input.aligned_sequences_fasta
Array[File]+ — Default: ["gs://nextstrain-data/files/ncov/open/aligned.fasta.zst"]
Set of assembled and aligned genomes to build trees. These must represent a single chromosome/segment of a genome only. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture.
sarscov2_nextstrain_aligned_input.ancestral_traits.confidence
Boolean — Default: true
???
sarscov2_nextstrain_aligned_input.ancestral_traits.disk_size
Int — Default: 750
???
sarscov2_nextstrain_aligned_input.ancestral_traits.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.ancestral_traits.machine_mem_gb
Int — Default: 32
???
sarscov2_nextstrain_aligned_input.ancestral_traits.sampling_bias_correction
Float? — Default: None
???
sarscov2_nextstrain_aligned_input.ancestral_traits.weights
File? — Default: None
???
sarscov2_nextstrain_aligned_input.ancestral_traits_to_infer
Array[String]? — Default: None
A list of metadata traits to use for ancestral node inference (see https://nextstrain-augur.readthedocs.io/en/stable/usage/cli/traits.html). Multiple traits may be specified; must correspond exactly to column headers in metadata file. Omitting these values will skip ancestral trait inference, and ancestral nodes will not have estimated values for metadata.
sarscov2_nextstrain_aligned_input.ancestral_tree.disk_size
Int — Default: 300
???
sarscov2_nextstrain_aligned_input.ancestral_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.ancestral_tree.infer_ambiguous
Boolean — Default: false
???
sarscov2_nextstrain_aligned_input.ancestral_tree.inference
String — Default: "joint"
???
sarscov2_nextstrain_aligned_input.ancestral_tree.keep_ambiguous
Boolean — Default: false
???
sarscov2_nextstrain_aligned_input.ancestral_tree.keep_overhangs
Boolean — Default: false
???
sarscov2_nextstrain_aligned_input.ancestral_tree.output_vcf
File? — Default: None
???
sarscov2_nextstrain_aligned_input.ancestral_tree.vcf_reference
File? — Default: None
???
sarscov2_nextstrain_aligned_input.assign_clades_to_nodes.disk_size
Int — Default: 300
???
sarscov2_nextstrain_aligned_input.assign_clades_to_nodes.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.augur_mask_sites.disk_size
Int — Default: 750
???
sarscov2_nextstrain_aligned_input.augur_mask_sites.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.augur_mask_sites.mask_bed
File? — Default: None
???
sarscov2_nextstrain_aligned_input.auspice_config
File? — Default: None
???
sarscov2_nextstrain_aligned_input.clades_tsv
File? — Default: None
A TSV file containing clade mutation positions in four columns: [clade gene site alt]; see: https://nextstrain.org/docs/tutorials/defining-clades
sarscov2_nextstrain_aligned_input.dedup_seqs.disk_size
Int — Default: 750
???
sarscov2_nextstrain_aligned_input.dedup_seqs.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.dedup_seqs.error_on_seq_diff
Boolean — Default: false
If error_on_seq_diff=true, an error will be raised if duplicate sequence IDs exist but have different sequences. By default, use the first occurrence of each duplicated sequence.
sarscov2_nextstrain_aligned_input.dedup_seqs.nextstrain_ncov_repo_commit
String — Default: "30435fb9ec8de2f045167fb90adfec12f123e80a"
???
sarscov2_nextstrain_aligned_input.derived_cols.disk_size
Int — Default: 50
???
sarscov2_nextstrain_aligned_input.derived_cols.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???
sarscov2_nextstrain_aligned_input.derived_cols.lab_highlight_loc
String? — Default: None
This option copies the 'originating_lab' and 'submitting_lab' columns to new ones including a prefix, but only if they match certain criteria. The value of this string must be of the form prefix;col_header=value:col_header=value. For example, 'MA;country=USA:division=Massachusetts' will copy the originating_lab and submitting_lab columns to MA_originating_lab and MA_submitting_lab, but only for those rows where country=USA and division=Massachusetts.
sarscov2_nextstrain_aligned_input.derived_cols.table_map
Array[File] — Default: []
Mapping tables. Each mapping table is a tsv with a header. The first column is the output column name for this mapping (it will be created or overwritten). The subsequent columns are matching criteria. The value in the first column is written to the output column. The exception is in the case where all match columns are '*' -- in this case, the value in the first column is the column header name to copy over.
sarscov2_nextstrain_aligned_input.draft_augur_tree.cpus
Int — Default: 64
???
sarscov2_nextstrain_aligned_input.draft_augur_tree.disk_size
Int — Default: 1250
???
sarscov2_nextstrain_aligned_input.draft_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.draft_augur_tree.exclude_sites
File? — Default: None
???
sarscov2_nextstrain_aligned_input.draft_augur_tree.machine_mem_gb
Int — Default: 32
???
sarscov2_nextstrain_aligned_input.draft_augur_tree.method
String — Default: "iqtree"
???
sarscov2_nextstrain_aligned_input.draft_augur_tree.substitution_model
String — Default: "GTR"
???
sarscov2_nextstrain_aligned_input.draft_augur_tree.tree_builder_args
String? — Default: None
???
sarscov2_nextstrain_aligned_input.draft_augur_tree.vcf_reference
File? — Default: None
???
sarscov2_nextstrain_aligned_input.export_auspice_json.color_by_metadata
Array[String]? — Default: None
???
sarscov2_nextstrain_aligned_input.export_auspice_json.colors_tsv
File? — Default: None
???
sarscov2_nextstrain_aligned_input.export_auspice_json.description_md
File? — Default: None
???
sarscov2_nextstrain_aligned_input.export_auspice_json.disk_size
Int — Default: 300
???
sarscov2_nextstrain_aligned_input.export_auspice_json.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.export_auspice_json.geo_resolutions
Array[String]? — Default: None
???
sarscov2_nextstrain_aligned_input.export_auspice_json.include_root_sequence
Boolean — Default: true
???
sarscov2_nextstrain_aligned_input.export_auspice_json.machine_mem_gb
Int — Default: 64
???
sarscov2_nextstrain_aligned_input.export_auspice_json.maintainers
Array[String]? — Default: None
???
sarscov2_nextstrain_aligned_input.export_auspice_json.title
String? — Default: None
???
sarscov2_nextstrain_aligned_input.lat_longs_tsv
File? — Default: None
???
sarscov2_nextstrain_aligned_input.nextstrain_ncov_defaults.disk_size
Int — Default: 50
???
sarscov2_nextstrain_aligned_input.nextstrain_ncov_defaults.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.nextstrain_ncov_defaults.nextstrain_ncov_repo_commit
String — Default: "30435fb9ec8de2f045167fb90adfec12f123e80a"
???
sarscov2_nextstrain_aligned_input.ref_fasta
File? — Default: None
A reference assembly (not included in aligned_sequences_fasta). Typically from NCBI RefSeq or similar.
sarscov2_nextstrain_aligned_input.refine_augur_tree.branch_length_inference
String? — Default: None
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.clock_filter_iqd
Int? — Default: 4
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.clock_rate
Float? — Default: None
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.clock_std_dev
Float? — Default: None
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.coalescent
String? — Default: None
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.covariance
Boolean? — Default: None
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.date_confidence
Boolean — Default: true
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.date_inference
String? — Default: "marginal"
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.disk_size
Int — Default: 750
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.divergence_units
String? — Default: "mutations"
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.gen_per_year
Int? — Default: None
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.keep_polytomies
Boolean — Default: false
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.keep_root
Boolean — Default: true
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.machine_mem_gb
Int — Default: 75
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.precision
Int? — Default: None
???
sarscov2_nextstrain_aligned_input.refine_augur_tree.vcf_reference
File? — Default: None
???
sarscov2_nextstrain_aligned_input.sample_metadata_tsvs
Array[File]+ — Default: ["gs://nextstrain-data/files/ncov/open/metadata.tsv.gz"]
Tab-separated metadata file that contain binning variables and values. Must contain all samples: output will be filtered to the IDs present in this file.
sarscov2_nextstrain_aligned_input.snp_sites.allow_wildcard_bases
Boolean — Default: true
???
sarscov2_nextstrain_aligned_input.snp_sites.disk_size
Int — Default: 750
???
sarscov2_nextstrain_aligned_input.snp_sites.docker
String — Default: "quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0"
???
sarscov2_nextstrain_aligned_input.subsample.disk_size
Int — Default: 750
???
sarscov2_nextstrain_aligned_input.subsample.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.subsample.drop_list
File? — Default: None
???
sarscov2_nextstrain_aligned_input.subsample.keep_list
File? — Default: None
???
sarscov2_nextstrain_aligned_input.subsample.machine_mem_gb
Int — Default: 50
???
sarscov2_nextstrain_aligned_input.subsample.nextstrain_ncov_repo_commit
String — Default: "30435fb9ec8de2f045167fb90adfec12f123e80a"
???
sarscov2_nextstrain_aligned_input.subsample.parameters_yaml
File? — Default: None
YAML-formatted nextstrain parameter override definitions. If this is not specified, we will use this as a default: https://github.com/nextstrain/ncov/blob/master/defaults/parameters.yaml
sarscov2_nextstrain_aligned_input.tip_frequencies.censored
Boolean — Default: false
???
sarscov2_nextstrain_aligned_input.tip_frequencies.disk_size
Int — Default: 200
???
sarscov2_nextstrain_aligned_input.tip_frequencies.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.tip_frequencies.include_internal_nodes
Boolean — Default: false
???
sarscov2_nextstrain_aligned_input.tip_frequencies.inertia
Float? — Default: None
???
sarscov2_nextstrain_aligned_input.tip_frequencies.machine_mem_gb
Int — Default: 64
???
sarscov2_nextstrain_aligned_input.tip_frequencies.max_date
Float? — Default: None
???
sarscov2_nextstrain_aligned_input.tip_frequencies.method
String — Default: "kde"
???
sarscov2_nextstrain_aligned_input.tip_frequencies.minimal_frequency
Float? — Default: None
???
sarscov2_nextstrain_aligned_input.tip_frequencies.stiffness
Float? — Default: None
???
sarscov2_nextstrain_aligned_input.tip_frequencies.wide_bandwidth
Float? — Default: None
???
sarscov2_nextstrain_aligned_input.translate_augur_tree.disk_size
Int — Default: 300
???
sarscov2_nextstrain_aligned_input.translate_augur_tree.docker
String — Default: "nextstrain/base:build-20230905T192825Z"
???
sarscov2_nextstrain_aligned_input.translate_augur_tree.genes
File? — Default: None
???
sarscov2_nextstrain_aligned_input.translate_augur_tree.vcf_reference
File? — Default: None
???
sarscov2_nextstrain_aligned_input.translate_augur_tree.vcf_reference_output
File? — Default: None
???
sarscov2_nextstrain_aligned_input.tree_root_seq_id
String? — Default: "Wuhan-Hu-1/2019"
???
sarscov2_nextstrain_aligned_input.tsv_join.out_suffix
String — Default: ".txt"
???
sarscov2_nextstrain_aligned_input.tsv_join.prefer_first
Boolean — Default: true
???
sarscov2_nextstrain_aligned_input.zcat.cpus
Int — Default: 4
???
4.65.2. Outputs¶
sarscov2_nextstrain_aligned_input.auspice_input_json
File
???
sarscov2_nextstrain_aligned_input.combined_assemblies
File
???
sarscov2_nextstrain_aligned_input.counts_by_group
Map[String,Int]
???
sarscov2_nextstrain_aligned_input.keep_list
File
???
sarscov2_nextstrain_aligned_input.masked_alignment
File
???
sarscov2_nextstrain_aligned_input.metadata_merged
File
???
sarscov2_nextstrain_aligned_input.ml_tree
File
???
sarscov2_nextstrain_aligned_input.node_data_jsons
Array[File]
???
sarscov2_nextstrain_aligned_input.root_sequence_json
File
???
sarscov2_nextstrain_aligned_input.sequences_kept
Int
???
sarscov2_nextstrain_aligned_input.subsampled_sequences
File
???
sarscov2_nextstrain_aligned_input.time_tree
File
???
sarscov2_nextstrain_aligned_input.tip_frequencies_json
File
???
sarscov2_nextstrain_aligned_input.unmasked_snps
File
???
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