Standardize usage of Snakemake's "config" variable

Retrieving config that is required should be done using the bracket
syntax.

Retrieving config with .get should always be done with a default value.

Snakefile

@@ -37,8 +37,8 @@ rule all:
 
 rule rename:
     input:
-        auspice_json=build_dir + f"/{config.get('build_name')}/tree.json",
-        root_sequence=build_dir + f"/{config.get('build_name')}/tree_root-sequence.json",
+        auspice_json=build_dir + f"/{config['build_name']}/tree.json",
+        root_sequence=build_dir + f"/{config['build_name']}/tree_root-sequence.json",
     output:
         auspice_json=auspice_dir + f"/{config.get('auspice_name','tree')}.json",
         root_sequence_json=auspice_dir
@@ -63,7 +63,7 @@ include: "workflow/snakemake_rules/chores.smk"
 include: "workflow/snakemake_rules/core.smk"
 
 
-if config.get("deploy_url"):
+if config.get("deploy_url", False):
 
     include: "workflow/snakemake_rules/nextstrain_automation.smk"
 

ingest/Snakefile

@@ -57,7 +57,7 @@ def _get_all_targets(wildcards):
             ]
         )
 
-    if config.get("trigger_rebuild"):
+    if config.get("trigger_rebuild", False):
         all_targets.append("data/trigger/rebuild.done")
 
     return all_targets
@@ -73,7 +73,7 @@ include: "workflow/snakemake_rules/transform.smk"
 include: "workflow/snakemake_rules/nextclade.smk"
 
 
-if config.get("upload"):
+if config.get("upload", False):
 
     include: "workflow/snakemake_rules/upload.smk"
 
@@ -83,6 +83,6 @@ if send_slack_notifications:
     include: "workflow/snakemake_rules/slack_notifications.smk"
 
 
-if config.get("trigger_rebuild"):
+if config.get("trigger_rebuild", False):
 
     include: "workflow/snakemake_rules/trigger_rebuild.smk"

workflow/snakemake_rules/chores.smk

@@ -15,7 +15,7 @@ rule update_example_data:
         sequences="example_data/sequences.fasta",
         metadata="example_data/metadata.tsv",
     params:
-        strain_id=config.get("strain_id_field"),
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur filter \

workflow/snakemake_rules/core.smk

@@ -32,7 +32,7 @@ rule exclude_bad:
     params:
         min_date=config["min_date"],
         min_length=config["min_length"],
-        strain_id=config.get("strain_id_field"),
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur filter \
@@ -81,7 +81,7 @@ rule filter:
         group_by=config.get("group_by", "--group-by clade lineage"),
         sequences_per_group=config["sequences_per_group"],
         other_filters=config.get("filters", ""),
-        strain_id=config.get("strain_id_field"),
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur filter \
@@ -236,7 +236,7 @@ rule refine:
         clock_std_dev=f"--clock-std-dev {config['clock_std_dev']}"
         if "clock_std_dev" in config
         else "",
-        strain_id=config.get("strain_id_field"),
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur refine \
@@ -312,7 +312,7 @@ rule traits:
     params:
         columns="country",
         sampling_bias_correction=3,
-        strain_id=config.get("strain_id_field"),
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur traits \
@@ -444,7 +444,7 @@ rule export:
         auspice_json=build_dir + "/{build_name}/raw_tree.json",
         root_sequence=build_dir + "/{build_name}/raw_tree_root-sequence.json",
     params:
-        strain_id=config.get("strain_id_field"),
+        strain_id=config["strain_id_field"],
     shell:
         """
         augur export v2 \
@@ -470,7 +470,7 @@ rule final_strain_name:
         auspice_json=build_dir + "/{build_name}/tree.json",
         root_sequence=build_dir + "/{build_name}/tree_root-sequence.json",
     params:
-        strain_id=config.get("strain_id_field"),
+        strain_id=config["strain_id_field"],
         display_strain_field=config.get("display_strain_field", "strain"),
     shell:
         """