Add GitHub Action for Nextclade annotations

.github/workflows/run-nextclade.yaml

@@ -0,0 +1,32 @@
+name: Run Nextclade on all sequences
+
+on:
+  workflow_dispatch:
+    inputs:
+      dockerImage:
+        description: "Specific container image to use for build (will override the default of `nextstrain build`)"
+        required: false
+        type: string
+
+jobs:
+  run-build:
+    permissions:
+      id-token: write
+    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
+    secrets: inherit
+    with:
+      runtime: aws-batch
+      env: |
+        NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.dockerImage }}
+      run: |
+        nextstrain build \
+          --detach \
+          --cpus 36 \
+          --memory 72gib \
+          --env AWS_ACCESS_KEY_ID \
+          --env AWS_SECRET_ACCESS_KEY \
+          . \
+          upload_all_nextclade_files \
+          -p \
+          --configfile profiles/nextclade.yaml \
+          --set-threads run_nextclade=12

Snakefile

@@ -4,6 +4,7 @@ from treetime.utils import numeric_date
 
 
 wildcard_constraints:
+    lineage = r'h1n1pdm|h3n2|vic|yam',
     segment = r'pb2|pb1|pa|ha|np|na|mp|ns',
     center = r'who|cdc|crick|niid|crick|vidrl',
     passage = r'cell|egg',

profiles/nextclade.yaml

@@ -0,0 +1,17 @@
+custom_rules:
+  - workflow/snakemake_rules/download_from_s3.smk
+  - profiles/nextclade/run-nextclade.smk
+
+s3_dst: "s3://nextstrain-data-private/files/workflows/seasonal-flu"
+
+segments:
+  - ha
+  - na
+
+builds:
+  h1n1pdm:
+    lineage: h1n1pdm
+  h3n2:
+    lineage: h3n2
+  vic:
+    lineage: vic

profiles/nextclade/run-nextclade.smk

@@ -0,0 +1,72 @@
+rule upload_all_nextclade_files:
+    input:
+        files=lambda wildcards: [
+            "data/upload/s3/{filetype}_{lineage}_{segment}.done".format(filetype=filetype, lineage=build["lineage"], segment=segment)
+            for filetype in ("alignment", "nextclade")
+            for build in config["builds"].values()
+            for segment in config["segments"]
+        ]
+
+rule get_nextclade_dataset_for_lineage_and_segment:
+    output:
+        nextclade_dir=directory("nextclade_dataset/{lineage}_{segment}/"),
+    shell:
+        """
+        nextclade3 dataset get \
+            -n flu_{wildcards.lineage}_{wildcards.segment} \
+            --output-dir {output.nextclade_dir}
+        """
+
+rule run_nextclade:
+    input:
+        nextclade_dir="nextclade_dataset/{lineage}_{segment}/",
+        sequences="data/{lineage}/{segment}.fasta",
+    output:
+        alignment="data/upload/s3/{lineage}/{segment}/aligned.fasta",
+        annotations="data/upload/s3/{lineage}/{segment}/nextclade.tsv",
+    log:
+        "logs/run_nextclade_{lineage}_{segment}.txt"
+    threads: 8
+    shell:
+        """
+        nextclade3 run \
+            -j {threads} \
+            -D {input.nextclade_dir} \
+            --output-fasta {output.alignment} \
+            --output-tsv {output.annotations} \
+            {input.sequences}
+        """
+
+rule upload_alignment:
+    input:
+        alignment="data/upload/s3/{lineage}/{segment}/aligned.fasta",
+    output:
+        flag="data/upload/s3/alignment_{lineage}_{segment}.done",
+    params:
+        s3_dst=config["s3_dst"],
+    log:
+        "logs/upload_alignment_{lineage}_{segment}.txt"
+    shell:
+        """
+        ./scripts/upload-to-s3 \
+            --quiet \
+            {input.alignment:q} \
+            {params.s3_dst:q}/{wildcards.lineage}/{wildcards.segment}/aligned.fasta.xz 2>&1 | tee {output.flag}
+        """
+
+rule upload_nextclade_annotations:
+    input:
+        annotations="data/upload/s3/{lineage}/{segment}/nextclade.tsv",
+    output:
+        flag="data/upload/s3/nextclade_{lineage}_{segment}.done",
+    params:
+        s3_dst=config["s3_dst"],
+    log:
+        "logs/upload_nextclade_annotations_{lineage}_{segment}.txt"
+    shell:
+        """
+        ./scripts/upload-to-s3 \
+            --quiet \
+            {input.annotations:q} \
+            {params.s3_dst:q}/{wildcards.lineage}/{wildcards.segment}/nextclade.tsv.xz 2>&1 | tee {output.flag}
+        """

workflow/snakemake_rules/core.smk

@@ -488,10 +488,10 @@ rule annotate_recency_of_submissions:
     output:
         node_data = "builds/{build_name}/recency.json",
     params:
-        submission_date_field=config["submission_date_field"],
-        date_bins=config["recency"]["date_bins"],
-        date_bin_labels=config["recency"]["date_bin_labels"],
-        upper_bin_label=config["recency"]["upper_bin_label"],
+        submission_date_field=config.get("submission_date_field"),
+        date_bins=config.get("recency", {}).get("date_bins"),
+        date_bin_labels=config.get("recency", {}).get("date_bin_labels"),
+        upper_bin_label=config.get("recency", {}).get("upper_bin_label"),
     conda: "../envs/nextstrain.yaml"
     benchmark:
         "benchmarks/recency_{build_name}.txt"

workflow/snakemake_rules/download_from_s3.smk

@@ -1,3 +1,6 @@
+ruleorder: download_parsed_sequences > parse
+ruleorder: download_parsed_metadata > annotate_metadata_with_reference_strains
+
 rule download_sequences:
     output:
         sequences="data/{lineage}/raw_{segment}.fasta"
@@ -19,3 +22,25 @@ rule download_titers:
         """
         aws s3 cp {params.s3_path} - | gzip -c -d > {output.titers}
         """
+
+rule download_parsed_sequences:
+    output:
+        sequences="data/{lineage}/{segment}.fasta"
+    params:
+        s3_path="s3://nextstrain-data-private/files/workflows/seasonal-flu/{lineage}/{segment}/sequences.fasta.xz"
+    conda: "../../workflow/envs/nextstrain.yaml"
+    shell:
+        """
+        aws s3 cp {params.s3_path} - | xz -c -d > {output.sequences}
+        """
+
+rule download_parsed_metadata:
+    output:
+        metadata="data/{lineage}/metadata.tsv",
+    params:
+        s3_path="s3://nextstrain-data-private/files/workflows/seasonal-flu/{lineage}/metadata.tsv.xz"
+    conda: "../../workflow/envs/nextstrain.yaml"
+    shell:
+        """
+        aws s3 cp {params.s3_path} - | xz -c -d > {output.metadata}
+        """

workflow/snakemake_rules/export.smk

@@ -59,7 +59,7 @@ rule export:
         metadata = build_dir + "/{build_name}/metadata.tsv",
         node_data = _get_node_data_by_wildcards,
         auspice_config = lambda w: config['builds'][w.build_name]['auspice_config'],
-        lat_longs = config['lat-longs']
+        lat_longs = config.get('lat-longs', "config/lat_longs.tsv"),
     output:
         auspice_json = "auspice/{build_name}_{segment}.json",
         root_sequence_json = "auspice/{build_name}_{segment}_root-sequence.json",