Jro mpxv global tree

[jrotieno]

🛠️ Changes Being Made

Adds a new workflow, Samples_to_Ref_Tree_PHB:
https://github.com/theiagen/public_health_bioinformatics/blob/jro_mpxv_global_tree/workflows/phylogenetics/wf_nextclade_addToRefTree.wdl

and a new nextclade task:
https://github.com/theiagen/public_health_bioinformatics/blob/jro_mpxv_global_tree/tasks/taxon_id/task_nextclade.wdl

🧠 Context and Rationale

The workflow allows the user to perform phylogenetic placement of a set of samples onto a global reference tree; the global tree could be from nextclade data using the default tree.json , or a user supplied auspice tree JSON.

📋 Workflow/Task Steps

Take a sample or set of samples, and place them onto a reference tree using nextclade. A nextclade dataset reference tree is used by default, unless a reference tree is supplied by the user.

Inputs

Required inputs:

1. assembly_fastas; A fasta file with query sequence(s) to be placed onto the global tree
2. organism; This will be in line with the Nextclade dataset names, and therefore the 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"

Optional inputs:
docker; nextclade docker image
dataset_reference; nextclade dataset reference sequence
dataset_tag; nextclade dataset tag
gene_annotations_gff; A genome annotations file for codon-aware alignment, gene translation and calling of aminoacid mutations
pcr_primers_csv; A file with a list of PCR primers used to detect changes in PCR primer regions
qc_config_json; A file with a set of parameters and thresholds used to configure the QC checks
reference_tree_json; A phylogenetic reference tree file which serves as a target for phylogenetic placement
root_sequence_fasta; A sequence which serves as a reference for alignment and the analysis
virus_properties; A configuration file that directs mutation labels

Outputs

treeUpdate_auspice_json; Output phylogenetic tree with user placed samples
treeUpdate_nextclade_docker; nextclade docker image used
treeUpdate_nextclade_json; JSON file with the results of the nextclade analysis
treeUpdate_nextclade_tsv; Tab-delimited file with nextclade results
treeUpdate_nextclade_version; nextclade version
samples_to_ref_tree_version ; PHB version
samples_to_ref_tree_analysis_date; Analysis date

🧪 Testing

Locally

Terra

The workflow has been tested on various nextclade pathogen datasets:
SARS-CoV-2; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/f9061e22-3246-459b-8617-9101f684e909
MPXV; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/d00d317f-0abe-4734-a769-9e447ee6beeb
RSV A; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/bcfcd389-2c91-4238-a083-2848d6baddd1
RSV B; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/4e22378b-3693-4eac-b693-806696220052
Influenza A H1N1pdm HA; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/e658c701-8676-4abe-b6ce-b2776086a5d2
Influenza A H1N1pdm NA; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/7786879b-ef9c-41cd-af75-c7cdf3110749
Influenza A H3N2 HA; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/7224d387-a107-4142-9e23-dd9891423d6c
Influenza A H3N2 NA; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/cb1c9e47-9c44-47cf-8a9b-5a58246aad05
Influenza B Victoria HA; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/2cfde037-1d6c-4f55-9e7b-ee083a39acfc
Influenza B Victoria NA; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/0f4d6b13-37ef-41f2-a2aa-ea8c97aebe83
Influenza B Yamagata HA; https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/Global_tree_testing/job_history/ae29b073-224b-4871-b30a-9b0b2db2d915

🔬 Quality checks

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The workflow/task has been tested locally and on Terra
• The CI/CD has been adjusted and tests are passing
• Everything follows the style guide

[emily-smith1]

Tested successfully on 10 individual SARS-CoV-2 genome assemblies. The outputs are as expected and the JSON files can be successfully loaded into Auspice.

[kevinlibuit]

@jrotieno curious to know the rationale for removing this default iqd? Seems to allow for the inclusion of very-poorly inferred dates