Harmonize ingest with pathogen repo guide

ingest/README.md

@@ -44,7 +44,12 @@ A pair of files for each dengue serotype (denv1 - denv4)
 Run the complete ingest pipeline and upload results to AWS S3 with
 
 ```sh
-nextstrain build ingest --configfiles config/config.yaml config/optional.yaml
+nextstrain build \
+    --env AWS_ACCESS_KEY_ID \
+    --env AWS_SECRET_ACCESS_KEY \
+    ingest \
+        upload_all \
+        --configfile build-configs/nextstrain-automation/config.yaml
 ```
 
 ### Adding new sequences not from GenBank
@@ -70,12 +75,12 @@ Do the following to include sequences from static FASTA files.
     !ingest/data/{file-name}.ndjson
     ```
 
-3. Add the `file-name` (without the `.ndjson` extension) as a source to `ingest/config/config.yaml`. This will tell the ingest pipeline to concatenate the records to the GenBank sequences and run them through the same transform pipeline.
+3. Add the `file-name` (without the `.ndjson` extension) as a source to `ingest/defaults/config.yaml`. This will tell the ingest pipeline to concatenate the records to the GenBank sequences and run them through the same transform pipeline.
 
 ## Configuration
 
-Configuration takes place in `config/config.yaml` by default.
-Optional configs for uploading files and Slack notifications are in `config/optional.yaml`.
+Configuration takes place in `defaults/config.yaml` by default.
+Optional configs for uploading files and Slack notifications are in `defaults/optional.yaml`.
 
 ### Environment Variables
 

ingest/Snakefile

@@ -4,10 +4,7 @@ min_version(
     "7.7.0"
 )  # Snakemake 7.7.0 introduced `retries` directive used in fetch-sequences
 
-if not config:
-
-    configfile: "config/config.yaml"
-
+configfile: "defaults/config.yaml"
 
 send_slack_notifications = config.get("send_slack_notifications", False)
 
@@ -57,12 +54,13 @@ rule all:
         _get_all_targets,
 
 
-include: "workflow/snakemake_rules/fetch_sequences.smk"
-include: "workflow/snakemake_rules/transform.smk"
-include: "workflow/snakemake_rules/split_serotypes.smk"
-include: "workflow/snakemake_rules/nextclade.smk"
-
+include: "rules/fetch_from_ncbi.smk"
+include: "rules/curate.smk"
+include: "rules/split_serotypes.smk"
+include: "rules/nextclade.smk"
 
-if config.get("upload", False):
+# Include custom rules defined in the config.
+if "custom_rules" in config:
+    for rule_file in config["custom_rules"]:
 
-    include: "workflow/snakemake_rules/upload.smk"
+        include: rule_file

ingest/build-configs/nextstrain-automation/config.yaml

@@ -0,0 +1,29 @@
+# This configuration file should contain all required configuration parameters
+# for the ingest workflow to run with additional Nextstrain automation rules.
+
+# Custom rules to run as part of the Nextstrain automated workflow
+# The paths should be relative to the ingest directory.
+custom_rules:
+  - build-configs/nextstrain-automation/upload.smk
+
+# Nextstrain CloudFront domain to ensure that we invalidate CloudFront after the S3 uploads
+# This is required as long as we are using the AWS CLI for uploads
+cloudfront_domain: "data.nextstrain.org"
+
+# Nextstrain AWS S3 Bucket with pathogen prefix
+s3_dst: "s3://nextstrain-data/files/workflows/dengue"
+
+# Mapping of files to upload
+files_to_upload:
+  genbank.ndjson.xz: data/genbank.ndjson
+  all_sequences.ndjson.xz: data/sequences.ndjson
+  metadata_all.tsv.zst: results/metadata_all.tsv
+  sequences_all.fasta.zst: results/sequences_all.fasta
+  metadata_denv1.tsv.zst: results/metadata_denv1.tsv
+  sequences_denv1.fasta.zst: results/sequences_denv1.fasta
+  metadata_denv2.tsv.zst: results/metadata_denv2.tsv
+  sequences_denv2.fasta.zst: results/sequences_denv2.fasta
+  metadata_denv3.tsv.zst: results/metadata_denv3.tsv
+  sequences_denv3.fasta.zst: results/sequences_denv3.fasta
+  metadata_denv4.tsv.zst: results/metadata_denv4.tsv
+  sequences_denv4.fasta.zst: results/sequences_denv4.fasta

ingest/build-configs/nextstrain-automation/upload.smk

@@ -0,0 +1,47 @@
+"""
+This part of the workflow handles uploading files to AWS S3.
+
+Files to upload must be defined in the `files_to_upload` config param, where
+the keys are the remote files and the values are the local filepaths
+relative to the ingest directory.
+
+Produces a single file for each uploaded file:
+    "results/upload/{remote_file}.upload"
+
+The rule `upload_all` can be used as a target to upload all files.
+"""
+import os
+
+slack_envvars_defined = "SLACK_CHANNELS" in os.environ and "SLACK_TOKEN" in os.environ
+send_notifications = (
+    config.get("send_slack_notifications", False) and slack_envvars_defined
+)
+
+
+rule upload_to_s3:
+    input:
+        file_to_upload=lambda wildcards: config["files_to_upload"][wildcards.remote_file],
+    output:
+        "results/upload/{remote_file}.upload",
+    params:
+        quiet="" if send_notifications else "--quiet",
+        s3_dst=config["s3_dst"],
+        cloudfront_domain=config["cloudfront_domain"],
+    shell:
+        """
+        ./vendored/upload-to-s3 \
+            {params.quiet} \
+            {input.file_to_upload:q} \
+            {params.s3_dst:q}/{wildcards.remote_file:q} \
+            {params.cloudfront_domain} 2>&1 | tee {output}
+        """
+
+
+rule upload_all:
+    input:
+        uploads=[
+            f"results/upload/{remote_file}.upload"
+            for remote_file in config["files_to_upload"].keys()
+        ],
+    output:
+        touch("results/upload_all.done")

ingest/config/config.yaml → ingest/defaults/config.yaml

@@ -23,28 +23,27 @@ ncbi_datasets_fields:
   - submitter-names
   - submitter-affiliation
 
-# Params for the transform rule
-transform:
+# Params for the curate rule
+curate:
   # NCBI Fields to rename to Nextstrain field names.
   # This is the first step in the pipeline, so any references to field names
   # in the configs below should use the new field names
-  field_map: [
-    'accession=genbank_accession',
-    'accession-rev=genbank_accession_rev',
-    'isolate-lineage=strain',
-    'sourcedb=database', # necessary for applying geo location rules
-    'geo-region=region',
-    'geo-location=location',
-    'host-name=host',
-    'isolate-collection-date=date',
-    'release-date=release_date',
-    'update-date=update_date',
-    'virus-tax-id=virus_tax_id',
-    'virus-name=virus_name',
-    'sra-accs=sra_accessions',    
-    'submitter-names=authors',
-    'submitter-affiliation=institution',
-  ]
+  field_map:
+    accession: genbank_accession
+    accession-rev: genbank_accession_rev
+    isolate-lineage: strain
+    sourcedb: database
+    geo-region: region
+    geo-location: location
+    host-name: host
+    isolate-collection-date: date
+    release-date: release_date
+    update-date: update_date
+    virus-tax-id: virus_tax_id
+    virus-name: virus_name
+    sra-accs: sra_accessions
+    submitter-names: authors
+    submitter-affiliation: institution
   # Standardized strain name regex
   # Currently accepts any characters because we do not have a clear standard for strain names
   strain_regex: '^.+$'
@@ -77,9 +76,9 @@ transform:
   geolocation_rules_url: 'https://raw.githubusercontent.com/nextstrain/ncov-ingest/master/source-data/gisaid_geoLocationRules.tsv'
   # Local geolocation rules that are only applicable to mpox data
   # Local rules can overwrite the general geolocation rules provided above
-  local_geolocation_rules: 'source-data/geolocation-rules.tsv'
+  local_geolocation_rules: 'defaults/geolocation-rules.tsv'
   # User annotations file
-  annotations: 'source-data/annotations.tsv'
+  annotations: 'defaults/annotations.tsv'
   # ID field used to merge annotations
   annotations_id: 'genbank_accession'
   # Field to use as the sequence ID in the FASTA file

ingest/workflow/snakemake_rules/transform.smk → ingest/rules/curate.smk

@@ -1,5 +1,5 @@
 """
-This part of the workflow handles transforming the data into standardized
+This part of the workflow handles curating the data into standardized
 formats and expects input file
 
     sequences_ndjson = "data/sequences.ndjson"
@@ -9,15 +9,15 @@ This will produce output files as
     metadata = "results/metadata_all.tsv"
     sequences = "results/sequences_all.fasta"
 
-Parameters are expected to be defined in `config.transform`.
+Parameters are expected to be defined in `config.curate`.
 """
 
 
 rule fetch_general_geolocation_rules:
     output:
         general_geolocation_rules="data/general-geolocation-rules.tsv",
     params:
-        geolocation_rules_url=config["transform"]["geolocation_rules_url"],
+        geolocation_rules_url=config["curate"]["geolocation_rules_url"],
     shell:
         """
         curl {params.geolocation_rules_url} > {output.general_geolocation_rules}
@@ -27,7 +27,7 @@ rule fetch_general_geolocation_rules:
 rule concat_geolocation_rules:
     input:
         general_geolocation_rules="data/general-geolocation-rules.tsv",
-        local_geolocation_rules=config["transform"]["local_geolocation_rules"],
+        local_geolocation_rules=config["curate"]["local_geolocation_rules"],
     output:
         all_geolocation_rules="data/all-geolocation-rules.tsv",
     shell:
@@ -36,32 +36,39 @@ rule concat_geolocation_rules:
         """
 
 
-rule transform:
+def format_field_map(field_map: dict[str, str]) -> str:
+    """
+    Format dict to `"key1"="value1" "key2"="value2"...` for use in shell commands.
+    """
+    return " ".join([f'"{key}"="{value}"' for key, value in field_map.items()])
+
+
+rule curate:
     input:
         sequences_ndjson="data/sequences.ndjson",
         all_geolocation_rules="data/all-geolocation-rules.tsv",
-        annotations=config["transform"]["annotations"],
+        annotations=config["curate"]["annotations"],
     output:
         metadata="data/metadata_all.tsv",
         sequences="results/sequences_all.fasta",
     log:
-        "logs/transform.txt",
+        "logs/curate.txt",
     params:
-        field_map=config["transform"]["field_map"],
-        strain_regex=config["transform"]["strain_regex"],
-        strain_backup_fields=config["transform"]["strain_backup_fields"],
-        date_fields=config["transform"]["date_fields"],
-        expected_date_formats=config["transform"]["expected_date_formats"],
-        articles=config["transform"]["titlecase"]["articles"],
-        abbreviations=config["transform"]["titlecase"]["abbreviations"],
-        titlecase_fields=config["transform"]["titlecase"]["fields"],
-        authors_field=config["transform"]["authors_field"],
-        authors_default_value=config["transform"]["authors_default_value"],
-        abbr_authors_field=config["transform"]["abbr_authors_field"],
-        annotations_id=config["transform"]["annotations_id"],
-        metadata_columns=config["transform"]["metadata_columns"],
-        id_field=config["transform"]["id_field"],
-        sequence_field=config["transform"]["sequence_field"],
+        field_map=format_field_map(config["curate"]["field_map"]),
+        strain_regex=config["curate"]["strain_regex"],
+        strain_backup_fields=config["curate"]["strain_backup_fields"],
+        date_fields=config["curate"]["date_fields"],
+        expected_date_formats=config["curate"]["expected_date_formats"],
+        articles=config["curate"]["titlecase"]["articles"],
+        abbreviations=config["curate"]["titlecase"]["abbreviations"],
+        titlecase_fields=config["curate"]["titlecase"]["fields"],
+        authors_field=config["curate"]["authors_field"],
+        authors_default_value=config["curate"]["authors_default_value"],
+        abbr_authors_field=config["curate"]["abbr_authors_field"],
+        annotations_id=config["curate"]["annotations_id"],
+        metadata_columns=config["curate"]["metadata_columns"],
+        id_field=config["curate"]["id_field"],
+        sequence_field=config["curate"]["sequence_field"],
     shell:
         """
         (cat {input.sequences_ndjson} \

ingest/workflow/snakemake_rules/nextclade.smk → ingest/rules/nextclade.smk

@@ -52,7 +52,7 @@ rule concat_nextclade_subtype_results:
     output:
         nextclade_subtypes="results/nextclade_subtypes.tsv",
     params:
-        id_field=config["transform"]["id_field"],
+        id_field=config["curate"]["id_field"],
         nextclade_field=config["nextclade"]["nextclade_field"],
     shell:
         """
@@ -75,7 +75,7 @@ rule append_nextclade_columns:
     output:
         metadata_all="results/metadata_all.tsv",
     params:
-        id_field=config["transform"]["id_field"],
+        id_field=config["curate"]["id_field"],
         nextclade_field=config["nextclade"]["nextclade_field"],
     shell:
         """

ingest/workflow/snakemake_rules/split_serotypes.smk → ingest/rules/split_serotypes.smk

@@ -9,7 +9,7 @@ This will produce output files as
 
     sequences_{serotype} = "results/sequences_{serotype}.fasta"
 
-Parameters are expected to be defined in `config.transform`.
+Parameters are expected to be defined in `config.curate`.
 """
 
 rule split_by_ncbi_serotype:
@@ -22,7 +22,7 @@ rule split_by_ncbi_serotype:
     output:
         sequences = "results/sequences_{serotype}.fasta"
     params:
-        id_field = config["transform"]["id_field"]
+        id_field = config["curate"]["id_field"]
     shell:
         """
         augur filter \