Add Nextclade and geo rules to example-data; disable "prM-E" build in phylo CI

ingest/build-configs/ci/copy_example_data.smk

@@ -1,12 +1,38 @@
-rule copy_example_data:
+rule copy_example_ncbi_data:
     input:
         ncbi_dataset="example-data/ncbi_dataset.zip"
     output:
         ncbi_dataset=temp("data/ncbi_dataset.zip")
     shell:
-        """
+        r"""
         cp -f {input.ncbi_dataset} {output.ncbi_dataset}
         """
-
 # force this rule over NCBI data fetch
-ruleorder: copy_example_data > fetch_ncbi_dataset_package
+ruleorder: copy_example_ncbi_data > fetch_ncbi_dataset_package
+
+
+DATASET_NAME = config["nextclade"]["dataset_name"]
+rule copy_example_nextclade_data:
+    input:
+        nextclade_dataset="example-data/nextclade_dataset.zip"
+    output:
+        nextclade_dataset=temp("data/nextclade_data/{DATASET_NAME}.zip")
+    shell:
+        r"""
+        cp -f {input.nextclade_dataset} {output.nextclade_dataset}
+        """
+# force this rule over Nextclade data fetch
+ruleorder: copy_example_nextclade_data > get_nextclade_dataset
+
+
+rule copy_example_geolocation_rules:
+    input:
+        general_geolocation_rules="example-data/general-geolocation-rules.tsv"
+    output:
+        general_geolocation_rules="data/general-geolocation-rules.tsv",
+    shell:
+        r"""
+        cp -f {input.general_geolocation_rules} {output.general_geolocation_rules}
+        """
+# force this rule over downloading geolocation rules
+ruleorder: copy_example_geolocation_rules > fetch_general_geolocation_rules

phylogenetic/Snakefile

@@ -1,11 +1,9 @@
 configfile: "defaults/config.yaml"
 
-gene = ["genome", "prM-E"]
-
 rule all:
     input:
-        auspice_json=expand("auspice/yellow-fever-virus_{gene}.json", gene=gene),
-        tip_frequencies_json=expand("auspice/yellow-fever-virus_{gene}_tip-frequencies.json", gene=gene),
+        auspice_json=expand("auspice/yellow-fever-virus_{build}.json", build=config["builds"]),
+        tip_frequencies_json=expand("auspice/yellow-fever-virus_{build}_tip-frequencies.json", build=config["builds"]),
 
 
 include: "rules/prepare_sequences.smk"

phylogenetic/build-configs/ci/config.yaml

@@ -1,2 +1,4 @@
+builds:
+  - "genome"
 custom_rules:
   - build-configs/ci/copy_example_data.smk

phylogenetic/defaults/config.yaml

@@ -1,3 +1,6 @@
+builds:
+    - "genome"
+    - "prM-E"
 strain_id_field: "accession"
 files:
     description: "defaults/description.md"

phylogenetic/rules/annotate_phylogeny.smk

@@ -6,16 +6,16 @@ phylogenetic tree.
 rule ancestral:
     """Reconstructing ancestral sequences and mutations"""
     input:
-        tree = "results/{gene}/tree.nwk",
-        alignment = "results/{gene}/aligned_and_filtered.fasta"
+        tree = "results/{build}/tree.nwk",
+        alignment = "results/{build}/aligned_and_filtered.fasta"
     output:
-        node_data = "results/{gene}/nt_muts.json"
+        node_data = "results/{build}/nt_muts.json"
     params:
         inference = config["ancestral"]["inference"]
     log:
-        "logs/{gene}/ancestral.txt",
+        "logs/{build}/ancestral.txt",
     benchmark:
-        "benchmarks/{gene}/ancestral.txt"
+        "benchmarks/{build}/ancestral.txt"
     shell:
         r"""
         augur ancestral \
@@ -29,15 +29,15 @@ rule ancestral:
 rule translate:
     """Translating amino acid sequences"""
     input:
-        tree = "results/{gene}/tree.nwk",
-        node_data = "results/{gene}/nt_muts.json",
-        genemap = "defaults/genemap_{gene}.gff"
+        tree = "results/{build}/tree.nwk",
+        node_data = "results/{build}/nt_muts.json",
+        genemap = "defaults/genemap_{build}.gff"
     output:
-        node_data = "results/{gene}/aa_muts.json"
+        node_data = "results/{build}/aa_muts.json"
     log:
-        "logs/{gene}/translate.txt",
+        "logs/{build}/translate.txt",
     benchmark:
-        "benchmarks/{gene}/translate.txt"
+        "benchmarks/{build}/translate.txt"
     shell:
         r"""
         augur translate \
@@ -52,17 +52,17 @@ rule translate:
 rule traits:
     """Inferring ancestral traits for {params.columns!s}"""
     input:
-        tree = "results/{gene}/tree.nwk",
+        tree = "results/{build}/tree.nwk",
         metadata = "data/metadata.tsv",
     output:
-        node_data = "results/{gene}/traits.json",
+        node_data = "results/{build}/traits.json",
     params:
         columns = config["traits"]["columns"],
         strain_id = config["strain_id_field"],
     log:
-        "logs/{gene}/traits.txt",
+        "logs/{build}/traits.txt",
     benchmark:
-        "benchmarks/{gene}/traits.txt"
+        "benchmarks/{build}/traits.txt"
     shell:
         r"""
         augur traits \

phylogenetic/rules/construct_phylogeny.smk

@@ -5,13 +5,13 @@ This part of the workflow constructs the phylogenetic tree.
 rule tree:
     """Building tree"""
     input:
-        alignment = "results/{gene}/aligned_and_filtered.fasta"
+        alignment = "results/{build}/aligned_and_filtered.fasta"
     output:
-        tree = "results/{gene}/tree_raw.nwk"
+        tree = "results/{build}/tree_raw.nwk"
     log:
-        "logs/{gene}/tree.txt",
+        "logs/{build}/tree.txt",
     benchmark:
-        "benchmarks/{gene}/tree.txt"
+        "benchmarks/{build}/tree.txt"
     shell:
         r"""
         augur tree \
@@ -28,24 +28,24 @@ rule refine:
       - filter tips more than {params.clock_filter_iqd} IQDs from clock expectation
     """
     input:
-        tree = "results/{gene}/tree_raw.nwk",
-        alignment = "results/{gene}/aligned_and_filtered.fasta",
+        tree = "results/{build}/tree_raw.nwk",
+        alignment = "results/{build}/aligned_and_filtered.fasta",
         metadata = "data/metadata.tsv"
     output:
-        tree = "results/{gene}/tree.nwk",
-        node_data = "results/{gene}/branch_lengths.json"
+        tree = "results/{build}/tree.nwk",
+        node_data = "results/{build}/branch_lengths.json"
     params:
         strain_id = config["strain_id_field"],
-        timetree = lambda w: "--timetree" if w.gene == "genome" else "",
+        timetree = lambda w: "--timetree" if w.build == "genome" else "",
         clock_rate = config["refine"]["clock_rate"],
         clock_std_dev = config["refine"]["clock_std_dev"],
         coalescent = config["refine"]["coalescent"],
         date_inference = config["refine"]["date_inference"],
         clock_filter_iqd = config["refine"]["clock_filter_iqd"],
     log:
-        "logs/{gene}/refine.txt",
+        "logs/{build}/refine.txt",
     benchmark:
-        "benchmarks/{gene}/refine.txt"
+        "benchmarks/{build}/refine.txt"
     shell:
         r"""
         augur refine \

phylogenetic/rules/export.smk

@@ -23,24 +23,24 @@ rule colors:
 rule export:
     """Exporting data files for for auspice"""
     input:
-        tree = "results/{gene}/tree.nwk",
+        tree = "results/{build}/tree.nwk",
         metadata = "data/metadata.tsv",
-        branch_lengths = "results/{gene}/branch_lengths.json",
-        nt_muts = "results/{gene}/nt_muts.json",
-        aa_muts = "results/{gene}/aa_muts.json",
-        traits = "results/{gene}/traits.json",
+        branch_lengths = "results/{build}/branch_lengths.json",
+        nt_muts = "results/{build}/nt_muts.json",
+        aa_muts = "results/{build}/aa_muts.json",
+        traits = "results/{build}/traits.json",
         colors = "data/colors.tsv",
-        auspice_config = lambda w: config["files"][w.gene]["auspice_config"],
+        auspice_config = lambda w: config["files"][w.build]["auspice_config"],
         description=config["files"]["description"],
     output:
-        auspice_json = "auspice/yellow-fever-virus_{gene}.json"
+        auspice_json = "auspice/yellow-fever-virus_{build}.json"
     params:
         metadata_columns = config["export"]["metadata_columns"],
         strain_id = config["strain_id_field"],
     log:
-        "logs/{gene}/export.txt",
+        "logs/{build}/export.txt",
     benchmark:
-        "benchmarks/{gene}/export.txt"
+        "benchmarks/{build}/export.txt"
     shell:
         r"""
         augur export v2 \
@@ -63,10 +63,10 @@ rule tip_frequencies:
     Estimating KDE frequencies for tips
     """
     input:
-        tree = "results/{gene}/tree.nwk",
+        tree = "results/{build}/tree.nwk",
         metadata = "data/metadata.tsv"
     output:
-        tip_freq = "auspice/yellow-fever-virus_{gene}_tip-frequencies.json"
+        tip_freq = "auspice/yellow-fever-virus_{build}_tip-frequencies.json"
     params:
         strain_id = config["strain_id_field"],
         min_date = config["tip_frequencies"]["min_date"],