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Include distances and explicit aa muts by default #630

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merged 2 commits into from
May 12, 2021
Merged

Include distances and explicit aa muts by default #630

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2839278
Include distances and explicit aa muts by default
huddlej May 10, 2021
165fe31
Update change log to reflect minor feature
huddlej May 12, 2021
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1 change: 1 addition & 0 deletions docs/change_log.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ We also use this change log to document new features that maintain backward comp

## New features since last version update

- 12 May 2021: Include S1 mutations and nextalign-based ancestral amino acid mutations in Auspice JSONs by default instead of requiring the now-unnecessary `use_nextalign` configuration parameter. ([#630](https://github.com/nextstrain/ncov/pull/630))
- 12 May 2021: [Document all available workflow configuration parameters](https://nextstrain.github.io/ncov/configuration). ([#633](https://github.com/nextstrain/ncov/pull/633))

## v5 (7 May 2021)
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7 changes: 3 additions & 4 deletions workflow/snakemake_rules/main_workflow.smk
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Expand Up @@ -1128,12 +1128,11 @@ def _get_node_data_by_wildcards(wildcards):
rules.clades.output.clade_data,
rules.recency.output.node_data,
rules.traits.output.node_data,
rules.logistic_growth.output.node_data
rules.logistic_growth.output.node_data,
rules.aa_muts_explicit.output.node_data,
rules.distances.output.node_data
]

if "use_nextalign" in config and config["use_nextalign"]:
inputs.append(rules.aa_muts_explicit.output.node_data)
inputs.append(rules.distances.output.node_data)
if "run_pangolin" in config and config["run_pangolin"]:
inputs.append(rules.make_pangolin_node_data.output.node_data)

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