diff --git a/Snakefile b/Snakefile index b6fe123..2c94dfa 100755 --- a/Snakefile +++ b/Snakefile @@ -19,6 +19,18 @@ if os.path.exists("config.yaml"): from pprint import pp; pp(config, stream=sys.stderr) # TODO XXX remove +# Before we validate the config against the schema, check to see if we've failed to provide one +if not len(config.keys()): + print("-"*80 + "\nNo config loaded!", file=sys.stderr) + print("Avian-flu is indented to be run from the snakefile inside a subdir " + "(e.g. gisaid/Snakefile) which will pick up the default configfile for that workflow. " + "Alternatively you can pass in the config via `--configfile`", file=sys.stderr) + print("-"*80, file=sys.stderr) + raise InvalidConfigError("No config") + +from scripts.validate_utils import validate +validate(config) + class InvalidConfigError(Exception): pass diff --git a/config/schema.yaml b/config/schema.yaml new file mode 100644 index 0000000..2a372de --- /dev/null +++ b/config/schema.yaml @@ -0,0 +1,375 @@ +$schema: http://json-schema.org/draft-07/schema# +type: object +title: Avian-flu config schema +description: > + This is the schema for the Nextstrain avian-flu phylogenetic workflow + . The readme (viewable at that URL) + provides general information including how to run the workflow. This schema + presents the interface into the phylogenetic workflow(s). +__aliases: + # We use YAML aliases to get the behaviour we want from $refs, namely we want the objects + # to be merged. This is not the case in draft-07 - any properties in an object with a '$ref' + # key are dropped. + generic_workflow_file: &generic_workflow_file + description: > + Relative path which is to be found in the analysis directory, the entry snakefile directory + (e.g. `avian-flu/gisaid`) or the workflow directory (`avian-flu`). First match is used. + File path which may include wildcards (see examples). + # NOTE: Some places where this is used provide their own description and thus this one isn't used. + type: string + # TODO: it's not clear whether spaces in filenames will work everywhere... + wildcard_param_property: &wildcard_param_property + # While the intention of the config is to distinguish between types (e.g. numbers, strings) + # In reality this doesn't matter _most_ of the time. We could create many such definitions to + # handle the combination of allowable types, but we can't pass in the type to this + # definition where it's used (e.g. via the $ref). + # Leaving this here as a potential TODO + oneOf: + - type: object + patternProperties: + "^[^_/]+/[^_/]+/[^_/]+$": + type: ['string', 'number', 'boolean', 'integer'] + description: &wildcard_param_property_wildcard_description > + An object to link wildcard values to the parameter to use. The keys are a `/`-separated + string of three parts corresponding to the subtype, segment and time wildcards. You can use + a `*` character for any part in order to match any wildcard value. For a given build this + object is searched for matching wildcard combinations, and the highest specificity key + is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then + we have a search order of: + - `h5nx/pb2/2y` ─ all 3 wildcard values specified + - `h5nx/pb2/*` ┐ + - `h5nx/*/2y` ├ 2/3 wildcard values specified + - `*/pb2/2y` ┘ + - `h5nx/*/*` ┐ + - `*/pb2/*` ├ 1/3 wildcard values specified + - `*/*/2y` ┘ + - `*/*/*` ─ default / fall-back + and the first key present in the config is used. + + The expected value type is dependant on the specific config parameter. + # Note: either YAML doesn't preserve multiple spaces or the generated HTML doesn't + # render them correctly + - type: ['string', 'number', 'boolean', 'integer'] + description: > + A scalar value which will be used for all builds, i.e. it does not change with + the wildcards. The type is dependant on the specific config parameter. +additionalProperties: False +required: + - builds + - target_patterns + - inputs + - subtype_lookup + - reference + - auspice_config + - colors + - lat_longs + - include_strains + - dropped_strains + - clades_file + - description + - filter + - refine + - ancestral + - traits + - export +properties: + builds: + title: Target subtype/segment/time combinations + description: > + Each element defines one or more subtypes, segments and time resolutions + which are expanded to produce all combinations. You can supply multiple elements + here in order to define different combinations. + + NOTE: H5N1 cattle-outbreak schemas should not define `time`. + examples: + - | + - subtype: + - h7n9 + - h9n2 + segment: + - ha + - na + time: + - all-time + type: array + items: + $ref: "#/$defs/build_element" + target_patterns: + default: "auspice/avian-flu_{subtype}_{segment}_{time}.json" + description: > + You can modify the target(s) the workflow will produce, using the `subtype`, `segment` and `time` wildcards which + will be filled in as per the builds the config defines. + Alternatively you can specify target filenames when you invoke the pipeline. + type: array + items: + type: string + minItems: 1 + custom_rules: + title: Additional snakefiles to include + description: > + TODO XXX describe where these can be located + type: array + items: + type: string + inputs: + title: Starting inputs + description: > + Commonly used by the base configs to define starting metadata/sequences on S3. + Override this if you don't want to use these canonical starting points, e.g. if you want to use locally ingested data. + type: array + items: + $ref: "#/$defs/input_item" + additional_inputs: + title: Additional starting inputs + description: > + Additional inputs. These will be merged with any `inputs` (see above) with the additional inputs taking priority. + See README for more information. + type: array + items: + $ref: "#/$defs/input_item" + subtype_lookup: + title: Mapping between wildcard subtype and metadata subtypes + description: > + The elements in each list are used by `augur filter` to filter the entire data + to produce metadata/sequences for each of the associated builds. + patternProperties: + "^(/[^/]+)+$": + type: array + minItems: 1 + items: + type: string + same_strains_per_segment: + description: > + When true we enforce each segment to use the same set of strains. + Not used for the h5n1-cattle-outbreak builds + type: boolean + reference: + title: Alignment reference (GenBank file) + description: > + align + FIX ME XXX + <<: *generic_workflow_file + auspice_config: + title: Auspice config JSON + <<: *generic_workflow_file + colors: + title: Colors TSV file + description: > + For GISAID builds this is used as augur export's `--colors` argument. + For h5n1-cattle-flu builds we additionally append colors which are not (yet) + config-definable. + <<: *generic_workflow_file + lat_longs: + title: Additional lat-longs + <<: *generic_workflow_file + include_strains: + title: TXT file listing strains which will be included + <<: *generic_workflow_file + dropped_strains: + title: TXT file listing strains which will be dropped + <<: *generic_workflow_file + clades_file: + title: H5 clades TSV file (H5 builds only) + <<: *generic_workflow_file + description: + title: Markdown file describing the footer shown in Auspice + <<: *generic_workflow_file + filter: + title: "Parameters for the filter step of the pipeline" + type: object + additionalProperties: False + required: + - target_sequences_per_tree + - min_length + - min_date + - group_by + - exclude_where + properties: + target_sequences_per_tree: + title: Target this many sequences per Auspice dataset + description: Augur filter `--subsample-max-sequences` value + <<: *wildcard_param_property + min_length: + title: Minimum length for sequences to be included + description: Augur filter `--min-length` value + <<: *wildcard_param_property + min_date: + title: Minimum date for sequences to be included + examples: + - "2y" + - 1996 + <<: *wildcard_param_property + group_by: + description: Augur filter `--group-by` value + <<: *wildcard_param_property + exclude_where: + description: Augur filter `--exclude-where` value + <<: *wildcard_param_property + refine: + title: "Parameters for the augur refine step of the pipeline" + type: object + additionalProperties: False + required: + - coalescent + - date_inference + - clock_filter_iqd + - clock_rates + - root + properties: + coalescent: + title: Coalescent time scale + description: > + Value passed to `augur refine --coalescent`. + <<: *wildcard_param_property + date_inference: + title: Date inference method + description: > + Value passed to `augur refine --date-inference`. + <<: *wildcard_param_property + clock_filter_iqd: + title: Filter out sequences which fall outside the inferred clock + description: > + Value passed to `augur refine --clock-filter-iqd`. If you supply a falsey + value then this argument not be provided. + <<: *wildcard_param_property + clock_rates: + title: Clock rate and std dev + oneOf: + - type: object + description: *wildcard_param_property_wildcard_description + patternProperties: + "^[^_/]+/[^_/]+/[^_/]+$": + $ref: "#/$defs/clock_rate_element" + - $ref: "#/$defs/clock_rate_element" + # Can't provide a description here as $ref will clobber it + root: + title: Root or rooting mechanism + description: > + Value passed to `augur refine --root`. If you supply a falsey + value then this argument not be provided. + <<: *wildcard_param_property + segment_lengths: + title: Sequence lengths for each segment + description: > + This option is only used for the `h5n1-cattle-outbreak` genome builds. + We use these values to calculate the clock-rate for the genome build from the suppied values + for each segment (via `clock_rates` config). + Values must be integers. + <<: *wildcard_param_property + ancestral: + title: "Parameters for the augur ancestral step of the pipeline" + type: object + additionalProperties: False + required: + - inference + - root_seq + properties: + inference: + title: Inference method + description: Passed to `augur ancestral --inference` + <<: *wildcard_param_property + root_seq: + title: Root sequence + description: > + Value passed to `augur ancestral --root-sequence`. If you supply a falsey + value then this argument not be provided. + <<: *wildcard_param_property + traits: + title: "Parameters for the augur traits step of the pipeline (DTA)" + type: object + additionalProperties: False + required: + - columns + - sampling_bias_correction + - confidence + properties: + columns: + title: DTA columns + description: > + Whitespace-separated columns on which to run `augur traits` + <<: *wildcard_param_property + sampling_bias_correction: + title: Sampling Bias Correction + description: > + Provide a falsey value to disable this correction, otherwise the provided value `X` is + passed as `augur traits --sampling-bias-correction X` + <<: *wildcard_param_property + confidence: + title: Infer confidence? + description: Value should be truthy or falsey + <<: *wildcard_param_property + export: + title: "Parameters for the augur export step of the pipeline" + description: "See also: `config.auspice_config`, above" + type: object + additionalProperties: False + required: + - title + properties: + title: + description: > + Use this property to override the auspice-config defined title. + Falsey values will use the auspice-config title. + <<: *wildcard_param_property +$defs: + string_or_array_of_strings: &string_or_array_of_strings + oneOf: + - type: string + - type: array + minItems: 1 + items: + type: string + build_element: + type: object + required: ['subtype', segment] + additionalProperties: False + properties: + subtype: + examples: + - H5N1 + - ['H5N1', 'H7N9'] + <<: *string_or_array_of_strings + segment: + examples: + - HA + - ['PB1', 'PB2'] + <<: *string_or_array_of_strings + time: + description: | + Note that this is unused for the h5n1-cattle-flu outbreak workflows + For GISAID workflows this is required. + examples: + - 2y + - ['all-time', '2y'] + <<: *string_or_array_of_strings + clock_rate_element: + description: The clock rate & std dev. Provide an empty string to infer this value instead. + oneOf: + - type: array + prefixItems: + - type: number + title: Clock rate (subs/site/year) + - type: number + title: Clock std dev + - enum: [''] + input_item: + type: object + required: ['name'] + properties: + name: + type: string + title: Name of the input + description: > + May be used in intermediate filepaths and in merged metadata columns. + Please avoid spaces. + metadata: + type: string + title: Metadata TSV filepath or S3 URI + sequences: + title: Sequence FASTA, 1 per segment + oneOf: + - type: string + title: Filepath/address with {segment} wildcard + - type: object + title: Map of segment name to filepath/address + diff --git a/public/schema.html b/public/schema.html new file mode 100644 index 0000000..ed71e41 --- /dev/null +++ b/public/schema.html @@ -0,0 +1,19 @@ + Avian-flu config schema

Avian-flu config schema

Type: object

This is the schema for the Nextstrain avian-flu phylogenetic workflow <https://github.com/nextstrain/avian-flu>. The readme (viewable at that URL) provides general information including how to run the workflow. This schema presents the interface into the phylogenetic workflow(s).

 No Additional Properties

root builds

Target subtype/segment/time combinations

Type: array

Each element defines one or more subtypes, segments and time resolutions which are expanded to produce all combinations. You can supply multiple elements here in order to define different combinations.
NOTE: H5N1 cattle-outbreak schemas should not define time.

 No Additional Items

Each item of this array must be:

root builds build_element
Type: object
No Additional Properties

root builds builds items subtype

root builds builds items subtype oneOf item 0
Type: string
root builds builds items subtype oneOf item 1
Type: array of string

Must contain a minimum of 1 items

No Additional Items

Each item of this array must be:

root builds builds items subtype oneOf item 1 item 1 items
Type: string

Examples:

"H5N1"
+
[
+    "H5N1",
+    "H7N9"
+]
+

root builds builds items segment

root builds builds items segment oneOf item 0
Type: string
root builds builds items segment oneOf item 1
Type: array of string

Must contain a minimum of 1 items

No Additional Items

Each item of this array must be:

root builds builds items segment oneOf item 1 item 1 items
Type: string

Examples:

"HA"
+
[
+    "PB1",
+    "PB2"
+]
+

root builds builds items time

Note that this is unused for the h5n1-cattle-flu outbreak workflows
For GISAID workflows this is required.

root builds builds items time oneOf item 0
Type: string
root builds builds items time oneOf item 1
Type: array of string

Must contain a minimum of 1 items

No Additional Items

Each item of this array must be:

root builds builds items time oneOf item 1 item 1 items
Type: string

Examples:

"2y"
+
[
+    "all-time",
+    "2y"
+]
+

Example:

"- subtype:\n    - h7n9\n    - h9n2\n  segment:\n    - ha\n    - na\n  time:\n    - all-time\n"
+

root target_patterns
Type: array of string Default: "auspice/avian-flu_{subtype}_{segment}_{time}.json"

You can modify the target(s) the workflow will produce, using the subtype, segment and time wildcards which will be filled in as per the builds the config defines. Alternatively you can specify target filenames when you invoke the pipeline.

Must contain a minimum of 1 items

No Additional Items

Each item of this array must be:

root target_patterns target_patterns items
Type: string

root custom_rules

Additional snakefiles to include

Type: array of string

TODO XXX describe where these can be located

 No Additional Items

Each item of this array must be:

root custom_rules custom_rules items
Type: string

root inputs

Starting inputs

Type: array

Commonly used by the base configs to define starting metadata/sequences on S3. Override this if you don't want to use these canonical starting points, e.g. if you want to use locally ingested data.

 No Additional Items

Each item of this array must be:

root inputs input_item
Type: object

root inputs inputs items name

Name of the input

Type: string

May be used in intermediate filepaths and in merged metadata columns. Please avoid spaces.

root inputs inputs items metadata

Metadata TSV filepath or S3 URI

Type: string

root inputs inputs items sequences

Sequence FASTA, 1 per segment


root additional_inputs

Additional starting inputs

Type: array

Additional inputs. These will be merged with any inputs (see above) with the additional inputs taking priority. See README for more information.

 No Additional Items

Each item of this array must be:

root additional_inputs input_item
Type: object
Same definition as inputs_items

root subtype_lookup

Mapping between wildcard subtype and metadata subtypes

Type: object

The elements in each list are used by augur filter to filter the entire data to produce metadata/sequences for each of the associated builds.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^(/[^/]+)+$
root subtype_lookup ^(/[^/]+)+$
Type: array of string

Must contain a minimum of 1 items

No Additional Items

Each item of this array must be:

root subtype_lookup ^(/[^/]+)+$ ^(/[^/]+)+$ items
Type: string

root same_strains_per_segment
Type: boolean

When true we enforce each segment to use the same set of strains. Not used for the h5n1-cattle-outbreak builds

root reference

Alignment reference (GenBank file)

Type: string

align FIX ME XXX

root auspice_config

Auspice config JSON

Type: string

Relative path which is to be found in the analysis directory, the entry snakefile directory (e.g. avian-flu/gisaid) or the workflow directory (avian-flu). First match is used. File path which may include wildcards (see examples).

root colors

Colors TSV file

Type: string

For GISAID builds this is used as augur export's --colors argument. For h5n1-cattle-flu builds we additionally append colors which are not (yet) config-definable.

root lat_longs

Additional lat-longs

Type: string

Relative path which is to be found in the analysis directory, the entry snakefile directory (e.g. avian-flu/gisaid) or the workflow directory (avian-flu). First match is used. File path which may include wildcards (see examples).

root include_strains

TXT file listing strains which will be included

Type: string

Relative path which is to be found in the analysis directory, the entry snakefile directory (e.g. avian-flu/gisaid) or the workflow directory (avian-flu). First match is used. File path which may include wildcards (see examples).

root dropped_strains

TXT file listing strains which will be dropped

Type: string

Relative path which is to be found in the analysis directory, the entry snakefile directory (e.g. avian-flu/gisaid) or the workflow directory (avian-flu). First match is used. File path which may include wildcards (see examples).

root clades_file

H5 clades TSV file (H5 builds only)

Type: string

Relative path which is to be found in the analysis directory, the entry snakefile directory (e.g. avian-flu/gisaid) or the workflow directory (avian-flu). First match is used. File path which may include wildcards (see examples).

root description

Markdown file describing the footer shown in Auspice

Type: string

Relative path which is to be found in the analysis directory, the entry snakefile directory (e.g. avian-flu/gisaid) or the workflow directory (avian-flu). First match is used. File path which may include wildcards (see examples).

root filter

Parameters for the filter step of the pipeline

Type: object
No Additional Properties

root filter target_sequences_per_tree

Target this many sequences per Auspice dataset


Augur filter --subsample-max-sequences value

root filter target_sequences_per_tree oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root filter target_sequences_per_tree oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root filter target_sequences_per_tree oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root filter min_length

Minimum length for sequences to be included


Augur filter --min-length value

root filter min_length oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root filter min_length oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root filter min_length oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root filter min_date

Minimum date for sequences to be included


root filter min_date oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root filter min_date oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root filter min_date oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

Examples:

"2y"
+
1996
+

root filter group_by

Augur filter --group-by value

root filter group_by oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root filter group_by oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root filter group_by oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root filter exclude_where

Augur filter --exclude-where value

root filter exclude_where oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root filter exclude_where oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root filter exclude_where oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root refine

Parameters for the augur refine step of the pipeline

Type: object
No Additional Properties

root refine coalescent

Coalescent time scale


Value passed to augur refine --coalescent.

root refine coalescent oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root refine coalescent oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root refine coalescent oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root refine date_inference

Date inference method


Value passed to augur refine --date-inference.

root refine date_inference oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root refine date_inference oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root refine date_inference oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root refine clock_filter_iqd

Filter out sequences which fall outside the inferred clock


Value passed to augur refine --clock-filter-iqd. If you supply a falsey value then this argument not be provided.

root refine clock_filter_iqd oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root refine clock_filter_iqd oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root refine clock_filter_iqd oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root refine clock_rates

Clock rate and std dev


root refine clock_rates oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root refine clock_rates oneOf item 0 clock_rate_element
Type: object

The clock rate & std dev. Provide an empty string to infer this value instead.

root refine clock_rates oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$ oneOf item 0
Type: array
No Additional Items

Tuple Validation

Item at 1 must be:
root refine clock_rates oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$ oneOf item 0 Clock rate (subs/site/year)

Clock rate (subs/site/year)

Type: number
Item at 2 must be:
root refine clock_rates oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$ oneOf item 0 Clock std dev

Clock std dev

Type: number
root refine clock_rates oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$ oneOf item 1
Type: enum (of string)

Must be one of:

  • ""
root refine clock_rates oneOf clock_rate_element
Type: object

The clock rate & std dev. Provide an empty string to infer this value instead.

Same definition as refine_clock_rates_oneOf_i0_pattern1

root refine root

Root or rooting mechanism


Value passed to augur refine --root. If you supply a falsey value then this argument not be provided.

root refine root oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root refine root oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root refine root oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root refine segment_lengths

Sequence lengths for each segment


This option is only used for the h5n1-cattle-outbreak genome builds. We use these values to calculate the clock-rate for the genome build from the suppied values for each segment (via clock_rates config). Values must be integers.

root refine segment_lengths oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root refine segment_lengths oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root refine segment_lengths oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root ancestral

Parameters for the augur ancestral step of the pipeline

Type: object
No Additional Properties

root ancestral inference

Inference method


Passed to augur ancestral --inference

root ancestral inference oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root ancestral inference oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root ancestral inference oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root ancestral root_seq

Root sequence


Value passed to augur ancestral --root-sequence. If you supply a falsey value then this argument not be provided.

root ancestral root_seq oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root ancestral root_seq oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root ancestral root_seq oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root traits

Parameters for the augur traits step of the pipeline (DTA)

Type: object
No Additional Properties

root traits columns

DTA columns


Whitespace-separated columns on which to run augur traits

root traits columns oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root traits columns oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root traits columns oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root traits sampling_bias_correction

Sampling Bias Correction


Provide a falsey value to disable this correction, otherwise the provided value X is passed as augur traits --sampling-bias-correction X

root traits sampling_bias_correction oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root traits sampling_bias_correction oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root traits sampling_bias_correction oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root traits confidence

Infer confidence?


Value should be truthy or falsey

root traits confidence oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root traits confidence oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root traits confidence oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.

root export

Parameters for the augur export step of the pipeline

Type: object

See also: config.auspice_config, above

 No Additional Properties

root export title

Use this property to override the auspice-config defined title. Falsey values will use the auspice-config title.

root export title oneOf item 0
Type: object

An object to link wildcard values to the parameter to use. The keys are a /-separated string of three parts corresponding to the subtype, segment and time wildcards. You can use a * character for any part in order to match any wildcard value. For a given build this object is searched for matching wildcard combinations, and the highest specificity key is chosen. Given example wildcard values of {subtype=h5nx, segment=pb2, time=2y} then we have a search order of:
- h5nx/pb2/2y ─ all 3 wildcard values specified
- h5nx/pb2/* ┐
- h5nx/*/2y ├ 2/3 wildcard values specified
- */pb2/2y ┘
- h5nx/*/* ┐
- */pb2/* ├ 1/3 wildcard values specified
- */*/2y ┘
- */*/* ─ default / fall-back
and the first key present in the config is used.
The expected value type is dependant on the specific config parameter.

All properties whose name matches the following regular expression must respect the following conditions

Property name regular expression: ^[^_/]+/[^_/]+/[^_/]+$
root export title oneOf item 0 ^[^_/]+/[^_/]+/[^_/]+$
Type: string, number, boolean or integer
root export title oneOf item 1
Type: string, number, boolean or integer

A scalar value which will be used for all builds, i.e. it does not change with the wildcards. The type is dependant on the specific config parameter.
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Error: {err}") + + # Here we're validating the merged schema. We could also validate the user config on its own by making (all?) properties optional? + from augur.validate import validate_json + validate_json(config, Validator(schema), "config") + + # There are more checks we can do by using code, as desired.