Nextclade_Batch¶
Quick Facts¶
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level | Dockstore |
|---|---|---|---|---|---|
| Phylogenetic Placement | Monkeypox virus, SARS-CoV-2, Viral | vX.X.X | Yes | Set-level | Nextclade_Batch_PHB |
Nextclade_Batch_PHB¶
Nextclade Batch rapidly calls mutations, places samples on a reference phylogenetic tree, and rapidly genotypes batches of samples using Nextclade. Phylogenetic placement is done by comparing the mutations of the query sequence (relative to the reference) with the mutations of every node and tip in the reference tree, and finding the node which has the most similar set of mutations. This operation is repeated for each query sequence, until all of them are placed onto the tree. This workflow uses the Nextstrain-maintained nextclade datasets for manually inputted datasets or downloaded datasets (e.g. SARS-CoV-2, mpox, influenza A and B, HIV, and RSV-A and RSV-B).
Contact us if you need help generating your own mutation-annotated tree, or follow the instructions available on the Augur wiki here.
Placement not construction
This workflow is not for building a tree from scratch, but rather for genotyping and placement of new sequences onto an existing high-quality input reference tree with representative samples on it. In effect, query samples are only compared to reference samples and never to the other query samples.
Inputs¶
| Terra Task Name | Variable | Type | Description | Default Value | Terra Status |
|---|---|---|---|---|---|
| nextclade_batch | assembly_fastas | Array[File] | The assembly files for your samples in FASTA format | Required | |
| nextclade_batch | dataset_name | String | What nextclade dataset name to run nextclade on; some options are: "sars-cov-2", "flu_h1n1pdm_ha", "flu_h1n1pdm_na", "flu_h3n2_ha", "flu_h3n2_na", "flu_vic_ha", "flu_vic_na", "flu_yam_ha", "hMPXV", "hMPXV_B1", "MPXV", "rsv_a" and "rsv_b" | Required | |
| nextclade_batch | dataset_tag | String | nextclade dataset tag | Uses the dataset tag associated with the nextclade docker image version | Optional |
| nextclade_batch | gene_annotations_gff | File | A genome annotations file for codon-aware alignment, gene translation and calling of amino acid mutations | Uses the genome annotation associated with the nextclade dataset name | Optional |
| nextclade_batch | input_ref | File | An optional FASTA file containing reference sequence. This file should contain exactly 1 sequence | Uses the reference fasta associated with the specified nextclade dataset name | Optional |
| nextclade_batch | pathogen_json | File | An optional pathogen JSON file containing configuration and data specific to a pathogen | Uses the reference pathogen JSON file associated with the specified nextclade dataset name | Optional |
| nextclade_batch | reference_tree_json | File | An optional phylogenetic reference tree file which serves as a target for phylogenetic placement | Uses the reference tree associated with the specified nextclade dataset name | Optional |
| nextclade_v3_set | cpu | Int | Number of CPUs to allocate to the task | 2 | Optional |
| nextclade_v3_set | disk_size | Int | Amount of storage (in GB) to allocate to the task | 100 | Optional |
| nextclade_v3_set | docker | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/nextstrain/nextclade:3.14.5 | Optional |
| nextclade_v3_set | memory | Int | Amount of memory/RAM (in GB) to allocate to the task | 4 | Optional |
| nextclade_v3_set | verbosity | String | Set the nextclade output verbosity level. Options: off, error, warn, info, debug, trace | warn | Optional |
| version_capture | docker | String | The Docker container to use for the task | us-docker.pkg.dev/general-theiagen/theiagen/alpine-plus-bash:3.20.0 | Optional |
| version_capture | timezone | String | Set the time zone to get an accurate date of analysis (uses UTC by default) | Optional |
Outputs¶
| Variable | Type | Description |
|---|---|---|
| nextclade_batch_analysis_date | String | Date of analysis |
| nextclade_batch_auspice_json | File | Phylogenetic tree with user placed samples |
| nextclade_batch_nextclade_docker | String | Nextclade docker image used |
| nextclade_batch_nextclade_json | File | JSON file with the results of the Nextclade analysis |
| nextclade_batch_nextclade_tsv | File | Tab-delimited file with Nextclade results |
| nextclade_batch_nextclade_version | String | Nextclade version used |
| nextclade_batch_version | String | Version of the Public Health Bioinformatics (PHB) repository used |