Use augur subsample

[victorlin]

Note

Based on #139 and nextstrain/augur#2037

Description of proposed changes

The previous subsampling implementation was fixed to a two-sample recent+background split with some hardcoded parameters. Replacing it with augur subsample allows for more flexible configuration.

In Snakemake, implementation is mostly copied from pathogen repos that have switched over to augur subsample. One notable difference is that the combine_samples rule must stay to handle output from the enrich_antibody_escape rule.

This is a breaking change and the old configuration will no longer work.

Related issue(s)

Closes #101

Checklist

• Update changelog
• Draft necessary changes on NW-PaGe fork: 0582db5
• Manually tested that validation fails with proximal sample entry
• Merge Configuration schema and validation #139 and Add schema def for unaligned sequences augur#2037
• Checks pass

old implementations

• YAML anchors and aliases: b0d6728
• matrix: d24a8d1
• dataset-first glob syntax 1: 5741f0f
• option-first glob syntax 1: bff7e53
• option-first glob syntax 2: 1df4e05
• dataset-first glob syntax 2: 397850d

[victorlin]

I'll wait for a decision in nextstrain/public#27 before continuing here.

[joverlee521]

Thank you for continuing to push through this! I've only added small comments for docs/changelog edits.

[joverlee521]

This is another instance where proximity subsampling is not supported so we should note it in the config/changelog (similar to rubella).

We're going to continuously run into this issue if we don't reorder workflows to align before subsample...I wonder if we should build a way to flag this in the subsample schema validation?

[victorlin]

Noted in changelog:

rsv/CHANGELOG.md

Line 8 in f9c14c2

* NOTE: The workflow does not yet support proximal samples.

I wonder if we should build a way to flag this in the subsample schema validation?

How would this work? Aligned and unaligned are both FASTA files. We'd have to inspect the actual sequences, and even then it's still a guess. The context of whether a FASTA is aligned or not lives at the workflow level.

[joverlee521]

Ah yeah, I'm thinking in the schema validation side only.

I think this would require making two schemas for augur subsample, one that includes proximalSampleProperties and the other without proximalSampleProperties. Then in the RSV workflow config schema, we'd reference the subsample schema that does not include proximalSampleProperties.

[victorlin]

Done using a def inside the existing subsample config schema:

rsv/config.schema.yaml

Lines 89 to 96 in 12efdc8

	subsample: &subsample_config
	<<: *per_full_build_map
	description: >-
	Subsampling configuration. When using --configfile, it is recommended to
	use 'custom_subsample' instead to ignore default subsampling configuration.
	patternProperties:
	"^.*$":
	$ref: "https://nextstrain.org/schemas/augur/subsample-config/v1#/$defs/schemaForUnalignedSequences"

This needed two additional PRs:

• Configuration schema and validation #139
• Add schema def for unaligned sequences augur#2037