Move rules for exporting auspice json to its own smk file

Part of work to update this repo to match the pathogen-repo-template.

phylogenetic/Snakefile

@@ -20,60 +20,7 @@ include: "workflow/snakemake_rules/usvi.smk"
 include: "workflow/snakemake_rules/prepare_sequences.smk"
 include: "workflow/snakemake_rules/construct_phylogeny.smk"
 include: "workflow/snakemake_rules/annotate_phylogeny.smk"
-
-rule export:
-    """Exporting data files for for auspice"""
-    input:
-        tree = "results/tree.nwk",
-        metadata = "data/metadata_all.tsv",
-        branch_lengths = "results/branch_lengths.json",
-        traits = "results/traits.json",
-        nt_muts = "results/nt_muts.json",
-        aa_muts = "results/aa_muts.json",
-        colors = files.colors,
-        auspice_config = files.auspice_config,
-        description = files.description
-    output:
-        auspice_json = "results/raw_zika.json",
-        root_sequence = "results/raw_zika_root-sequence.json",
-    params:
-        strain_id = config.get("strain_id_field", "strain"),
-    shell:
-        """
-        augur export v2 \
-            --tree {input.tree} \
-            --metadata {input.metadata} \
-            --metadata-id-columns {params.strain_id} \
-            --node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} \
-            --colors {input.colors} \
-            --auspice-config {input.auspice_config} \
-            --description {input.description} \
-            --include-root-sequence \
-            --output {output.auspice_json}
-        """
-
-rule final_strain_name:
-    input:
-        auspice_json="results/raw_zika.json",
-        metadata="data/metadata_all.tsv",
-        root_sequence="results/raw_zika_root-sequence.json",
-    output:
-        auspice_json="auspice/zika.json",
-        root_sequence="auspice/zika_root-sequence.json",
-    params:
-        strain_id=config["strain_id_field"],
-        display_strain_field=config.get("display_strain_field", "strain"),
-    shell:
-        """
-        python3 scripts/set_final_strain_name.py \
-            --metadata {input.metadata} \
-            --metadata-id-columns {params.strain_id} \
-            --input-auspice-json {input.auspice_json} \
-            --display-strain-name {params.display_strain_field} \
-            --output {output.auspice_json}
-
-        cp {input.root_sequence} {output.root_sequence}
-        """
+include: "workflow/snakemake_rules/export.smk"
 
 rule clean:
     """Removing directories: {params}"""

phylogenetic/workflow/snakemake_rules/export.smk

@@ -0,0 +1,80 @@
+"""
+This part of the workflow collects the phylogenetic tree and annotations to
+export a Nextstrain dataset.
+
+REQUIRED INPUTS:
+
+    metadata        = data/metadata_all.tsv
+    tree            = results/tree.nwk
+    branch_lengths  = results/branch_lengths.json
+    node_data       = results/*.json
+
+OUTPUTS:
+
+    auspice_json = auspice/${build_name}.json
+
+    There are optional sidecar JSON files that can be exported as part of the dataset.
+    See Nextstrain's data format docs for more details on sidecar files:
+    https://docs.nextstrain.org/page/reference/data-formats.html
+
+This part of the workflow usually includes the following steps:
+
+    - augur export v2
+    - augur frequencies
+
+See Augur's usage docs for these commands for more details.
+"""
+
+rule export:
+    """Exporting data files for for auspice"""
+    input:
+        tree = "results/tree.nwk",
+        metadata = "data/metadata_all.tsv",
+        branch_lengths = "results/branch_lengths.json",
+        traits = "results/traits.json",
+        nt_muts = "results/nt_muts.json",
+        aa_muts = "results/aa_muts.json",
+        colors = files.colors,
+        auspice_config = files.auspice_config,
+        description = files.description
+    output:
+        auspice_json = "results/raw_zika.json",
+        root_sequence = "results/raw_zika_root-sequence.json",
+    params:
+        strain_id = config.get("strain_id_field", "strain"),
+    shell:
+        """
+        augur export v2 \
+            --tree {input.tree} \
+            --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
+            --node-data {input.branch_lengths} {input.traits} {input.nt_muts} {input.aa_muts} \
+            --colors {input.colors} \
+            --auspice-config {input.auspice_config} \
+            --description {input.description} \
+            --include-root-sequence \
+            --output {output.auspice_json}
+        """
+
+rule final_strain_name:
+    input:
+        auspice_json="results/raw_zika.json",
+        metadata="data/metadata_all.tsv",
+        root_sequence="results/raw_zika_root-sequence.json",
+    output:
+        auspice_json="auspice/zika.json",
+        root_sequence="auspice/zika_root-sequence.json",
+    params:
+        strain_id=config["strain_id_field"],
+        display_strain_field=config.get("display_strain_field", "strain"),
+    shell:
+        """
+        python3 scripts/set_final_strain_name.py \
+            --metadata {input.metadata} \
+            --metadata-id-columns {params.strain_id} \
+            --input-auspice-json {input.auspice_json} \
+            --display-strain-name {params.display_strain_field} \
+            --output {output.auspice_json}
+
+        cp {input.root_sequence} {output.root_sequence}
+        """