nextstrain.org/rsv

This is the Nextstrain build for respiratory syncytial virus (RSV). Output from this build is available at https://nextstrain.org/rsv.

Data use

The default builds start from the public Nextstrain data that have been preprocessed and cleaned from Pathoplexus that includes RESTRICTED data. Please see Pathoplexus data use terms.

We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances.

Software requirements

Follow the standard installation instructions for Nextstrain's suite of software tools.

Usage

If you're unfamiliar with Nextstrain builds, you may want to follow our Running a Pathogen Workflow guide first and then come back here.

With nextstrain build

If you don't have a local copy of the rsv repository, use Git to download it

git clone https://github.com/nextstrain/rsv.git

Otherwise, update your local copy of the workflow with:

cd rsv
git pull --ff-only origin master

Run the phylogenetic workflow workflow with

nextstrain build .

The workflow's intermediate files will be output to results/ and the final outputs will be in auspice/.

Once you've run the build, you can view the results with:

nextstrain view .

Configuration

The default configuration is in config/configfile.yaml. The workflow is contained in the Snakefile with included rules. Each rule specifies its file inputs and outputs and pulls its parameters from the config. There is little redirection and each rule should be able to be reasoned with on its own.

Default input data

The default builds start from the public Nextstrain data that have been preprocessed and cleaned from Pathoplexus that includes RESTRICTED data. The default auspice_config.json includes the metadata_columns "PPX_accession", "INSDC_accession", and "restrictedUntil" to ensure the builds adhere to the Pathoplexus data use terms.

subtypes: ['a', 'b']
inputs:
  - name: ppx_with_restricted
    metadata: "https://data.nextstrain.org/files/workflows/rsv/{a_or_b}/metadata_with_restricted.tsv.gz"
    sequences: "https://data.nextstrain.org/files/workflows/rsv/{a_or_b}/sequences_with_restricted.fasta.xz"

Note the inputs require the {a_or_b} expandable field, to be replaced by the config parameter subtypes values.

Adding your own data

If you want to add your own data to the default input, specify your inputs with the additional_inputs config parameter. For example, this repo has a small set of example data that could be added to the default inputs via:

additional_inputs:
  - name: example-data
    metadata: example_data/{a_or_b}/metadata.tsv
    sequences: example_data/{a_or_b}/sequences.fasta

Note that the additional inputs also require the {a_or_b} expandable field. If you only have data for a single subtype, then you can do so with

serotypes: ["a"]
additional_inputs:
  - name: private
    metadata: private/a/metadata.tsv
    sequences: private/a/sequences.fasta

If you want to run the builds without the default data and only use your own data, you can do so by specifying the inputs parameter.

inputs:
  - name: example-data
    metadata: example_data/{a_or_b}/metadata.tsv
    sequences: example_data/{a_or_b}/sequences.fasta

Using locally ingested data

Run the ingest pipeline locally with

nextstrain build ingest

Then you can point the phylogenetic workflow to run from the produced results with

inputs:
    - name: local_ingest
      metadata: "ingest/data/{a_or_b}/metadata.tsv"
      sequences: "ingest/data/{a_or_b}/sequences.fasta"

shared/vendored

This repository uses git subrepo to manage copies of shared scripts in shared/vendored, from nextstrain/shared. See shared/vendored/README.md for instructions on how to update the vendored scripts.

Update example data

Example data is used by CI. It can also be used as a small subset of real-world data.

Example data should be updated every time metadata schema is changed. To update, run:

nextstrain build --docker . update_example_data --configfile config/chores.yaml -F

Sending data to the nextclade_data repo

From within the destination directory, run

rsync -a <path-to>/rsv/nextclade/datasets/ .