Misc tpyoes

ingest/Snakefile

@@ -12,7 +12,7 @@ configfile: "defaults/config.yaml"
 # The default output of the ingest workflow is usually the curated metadata and sequences.
 # Nextstrain-maintained ingest workflows will produce metadata files with the
 # standard Nextstrain fields and additional fields that are pathogen specific.
-# We recommend use these standard fields in custom ingests as well to minimize
+# We recommend using these standard fields in custom ingests as well to minimize
 # the customizations you will need for the downstream phylogenetic workflow.
 # TODO: Add link to centralized docs on standard Nextstrain metadata fields
 rule all:
@@ -60,7 +60,7 @@ else:
 # Allow users to import custom rules provided via the config.
 # This allows users to run custom rules that can extend or override the workflow.
 # A concrete example of using custom rules is the extension of the workflow with
-# rules to support the Nextstrain automation that upload files and send internal
+# rules to support the Nextstrain automation that uploads files and sends internal
 # Slack notifications.
 # For extensions, the user will have to specify the custom rule targets when
 # running the workflow.

ingest/defaults/config.yaml

@@ -11,7 +11,7 @@ entrez_search_term: ""
 ncbi_taxon_id: ""
 
 # The list of NCBI Datasets fields to include from NCBI Datasets output
-# These need to be the mneumonics of the NCBI Datasets fields, see docs for full list of fields
+# These need to be the mnemonics of the NCBI Datasets fields, see docs for full list of fields
 # https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_virus-genome/#fields
 # Note: the "accession" field MUST be provided to match with the sequences
 ncbi_datasets_fields:

ingest/rules/fetch_from_ncbi.smk

@@ -27,7 +27,7 @@ to provide the correct parameter.
 """
 
 # This ruleorder determines which rule to use to produce the final NCBI NDJSON file.
-# The default is set to use NCBI Datasets since it does no require a custom script.
+# The default is set to use NCBI Datasets since it does not require a custom script.
 # Switch the rule order if you plan to use Entrez
 ruleorder: format_ncbi_datasets_ndjson > parse_genbank_to_ndjson
 

phylogenetic/Snakefile

@@ -1,6 +1,6 @@
 """
 This is the main phylogenetic Snakefile that orchestrates the full phylogenetic
-workflow and define its default output(s).
+workflow and defines its default output(s).
 """
 # The workflow filepaths are written relative to this Snakefile's base directory
 workdir: workflow.current_basedir
@@ -11,7 +11,7 @@ configfile: "defaults/config.yaml"
 
 # This is the default rule that Snakemake will run when there are no specified targets.
 # The default output of the phylogenetic workflow is usually the final
-# Nexstrain dataset(s) or Auspice JSON(s) that is output from `rules/export.smk`
+# Nexstrain dataset(s) or Auspice JSON(s) that are output from `rules/export.smk`
 # See Nextstrain docs on expected naming conventions of dataset files
 # https://docs.nextstrain.org/page/reference/data-formats.html
 rule all: