Use "accession" column as ID column directly

New options in Augur 22.1.0 allow usage of this column as the ID column
across all subcommands that read metadata.

For this workflow in particular, the metadata file can now be used
as-is. This removes the need for a modified copy of the metadata. It
also allows specifying an original metadata column "strain" as the
display strain field, rather than a column "strain_original" generated
during the Snakemake workflow.

config/configfile.yaml

@@ -9,7 +9,7 @@ exclude: "config/outliers.txt"
 description: "config/description.md"
 
 strain_id_field: "accession"
-display_strain_field: "strain_original"
+display_strain_field: "strain"
 
 subtypes: ['a', 'b']
 

workflow/envs/nextstrain.yaml

@@ -19,6 +19,6 @@ dependencies:
  - pip
  - pip:
  - awscli==1.18.45
- - nextstrain-augur==11.3.0
+ - nextstrain-augur==22.1.0
  - nextstrain-cli==1.16.5
  - rethinkdb==2.3.0.post6

workflow/snakemake_rules/core.smk

@@ -4,20 +4,6 @@ This part of the workflow expects input files
  metadata = "data/metadata.tsv"
 '''
 
-rule wrangle_metadata:
- input:
- metadata="data/{a_or_b}/metadata.tsv",
- output:
- metadata="data/{a_or_b}/metadata_by_accession.tsv",
- params:
- strain_id=lambda w: config.get("strain_id_field", "strain"),
- shell:
- """
- python3 scripts/wrangle_metadata.py --metadata {input.metadata} \
- --strain-id {params.strain_id} \
- --output {output.metadata}
- """
-
 rule index_sequences:
  message:
  """
@@ -64,21 +50,23 @@ rule filter:
  input:
  sequences = "data/{a_or_b}/sequences.fasta",
  reference = "config/{a_or_b}reference.gbk",
- metadata = "data/{a_or_b}/metadata_by_accession.tsv",
+ metadata = "data/{a_or_b}/metadata.tsv",
  sequence_index = rules.index_sequences.output,
  exclude = config['exclude']
  output:
  sequences = build_dir + "/{a_or_b}/{build_name}/filtered.fasta"
  params:
  group_by = config["filter"]["group_by"],
  min_coverage = lambda w: f'{w.build_name}_coverage>{config["filter"]["min_coverage"].get(w.build_name, 10000)}',
- subsample_max_sequences = lambda w: config["filter"]["subsample_max_sequences"].get(w.build_name, 1000)
+ subsample_max_sequences = lambda w: config["filter"]["subsample_max_sequences"].get(w.build_name, 1000),
+ strain_id=lambda w: config.get("strain_id_field", "strain"),
  shell:
  """
  augur filter \
  --sequences {input.sequences} \
  --sequence-index {input.sequence_index} \
  --metadata {input.metadata} \
+ --metadata-id-columns {params.strain_id} \
  --exclude {input.exclude} \
  --output {output.sequences} \
  --group-by {params.group_by} \
@@ -196,13 +184,15 @@ rule refine:
  params:
  coalescent = config["refine"]["coalescent"],
  clock_filter_iqd = config["refine"]["clock_filter_iqd"],
- date_inference = config["refine"]["date_inference"]
+ date_inference = config["refine"]["date_inference"],
+ strain_id=lambda w: config.get("strain_id_field", "strain"),
  shell:
  """
  augur refine \
  --tree {input.tree} \
  --alignment {input.alignment} \
  --metadata {input.metadata} \
+ --metadata-id-columns {params.strain_id} \
  --output-tree {output.tree} \
  --output-node-data {output.node_data} \
  --coalescent {params.coalescent} \
@@ -264,12 +254,14 @@ rule traits:
  log:
  "logs/{a_or_b}/traits_{build_name}_rsv.txt"
  params:
- columns = config["traits"]["columns"]
+ columns = config["traits"]["columns"],
+ strain_id=lambda w: config.get("strain_id_field", "strain"),
  shell:
  """
  augur traits \
  --tree {input.tree} \
  --metadata {input.metadata} \
+ --metadata-id-columns {params.strain_id} \
  --output {output.node_data} \
  --columns {params.columns} \
  --confidence

workflow/snakemake_rules/export.smk

@@ -40,12 +40,14 @@ rule export:
  auspice_json = build_dir + "/{a_or_b}/{build_name}/tree.json",
  root_sequence = build_dir + "/{a_or_b}/{build_name}/tree_root-sequence.json"
  params:
- title = lambda w: f"RSV-{w.a_or_b.upper()} phylogeny"
+ title = lambda w: f"RSV-{w.a_or_b.upper()} phylogeny",
+ strain_id=lambda w: config.get("strain_id_field", "strain"),
  shell:
  """
  augur export v2 \
  --tree {input.tree} \
  --metadata {input.metadata} \
+ --metadata-id-columns {params.strain_id} \
  --node-data {input.node_data} \
  --title {params.title:q} \
  --description {input.description} \