phylo: update rule inputs to literal paths

Follow the Nextstrain Snakemake style guide¹ to use literal path strings
as inputs for the core workflow rules.

This will make it possible for users to override the default workflow
with `custom_rules`.

¹ https://docs.nextstrain.org/en/latest/reference/snakemake-style-guide.html#define-input-paths-with-literal-path-strings

phylogenetic/rules/annotate_phylogeny.smk

@@ -25,7 +25,7 @@ rule ancestral:
     Reconstructing ancestral sequences and mutations
     """
     input:
-        tree=rules.refine.output.tree,
+        tree=build_dir + "/{build_name}/tree.nwk",
         alignment=build_dir + "/{build_name}/masked.fasta",
     output:
         node_data=build_dir + "/{build_name}/nt_muts.json",
@@ -46,8 +46,8 @@ rule translate:
     Translating amino acid sequences
     """
     input:
-        tree=rules.refine.output.tree,
-        node_data=rules.ancestral.output.node_data,
+        tree=build_dir + "/{build_name}/tree.nwk",
+        node_data=build_dir + "/{build_name}/nt_muts.json",
         genemap=config["genemap"],
     output:
         node_data=build_dir + "/{build_name}/aa_muts.json",
@@ -67,7 +67,7 @@ rule traits:
       - increase uncertainty of reconstruction by {params.sampling_bias_correction} to partially account for sampling bias
     """
     input:
-        tree=rules.refine.output.tree,
+        tree=build_dir + "/{build_name}/tree.nwk",
         metadata=build_dir + "/{build_name}/metadata.tsv",
     output:
         node_data=build_dir + "/{build_name}/traits.json",
@@ -93,9 +93,9 @@ rule clades:
     Adding internal clade labels
     """
     input:
-        tree=rules.refine.output.tree,
-        aa_muts=rules.translate.output.node_data,
-        nuc_muts=rules.ancestral.output.node_data,
+        tree=build_dir + "/{build_name}/tree.nwk",
+        aa_muts=build_dir + "/{build_name}/aa_muts.json",
+        nuc_muts=build_dir + "/{build_name}/nt_muts.json",
         clades=config["clades"],
     output:
         node_data=build_dir + "/{build_name}/clades_raw.json",
@@ -113,7 +113,7 @@ rule clades:
 
 rule rename_clades:
     input:
-        rules.clades.output.node_data,
+        build_dir + "/{build_name}/clades_raw.json",
     output:
         node_data=build_dir + "/{build_name}/clades.json",
     shell:
@@ -126,7 +126,7 @@ rule rename_clades:
 
 rule mutation_context:
     input:
-        tree=rules.refine.output.tree,
+        tree=build_dir + "/{build_name}/tree.nwk",
         node_data=build_dir + "/{build_name}/nt_muts.json",
     output:
         node_data=build_dir + "/{build_name}/mutation_context.json",

phylogenetic/rules/construct_phylogeny.smk

@@ -41,7 +41,7 @@ rule fix_tree:
     Fixing tree
     """
     input:
-        tree=rules.tree.output.tree,
+        tree=build_dir + "/{build_name}/tree_raw.nwk",
         alignment=build_dir + "/{build_name}/masked.fasta",
     output:
         tree=build_dir + "/{build_name}/tree_fixed.nwk",
@@ -66,9 +66,9 @@ rule refine:
         - filter tips more than {params.clock_filter_iqd} IQDs from clock expectation
     """
     input:
-        tree=rules.fix_tree.output.tree
+        tree=build_dir + "/{build_name}/tree_fixed.nwk"
         if config["fix_tree"]
-        else rules.tree.output.tree,
+        else build_dir + "/{build_name}/tree_raw.nwk",
         alignment=build_dir + "/{build_name}/masked.fasta",
         metadata=build_dir + "/{build_name}/metadata.tsv",
     output:

phylogenetic/rules/export.smk

@@ -63,18 +63,18 @@ rule export:
     Exporting data files for auspice
     """
     input:
-        tree=rules.refine.output.tree,
+        tree=build_dir + "/{build_name}/tree.nwk",
         metadata=build_dir + "/{build_name}/metadata.tsv",
         branch_lengths="results/{build_name}/branch_lengths.json"
         if config.get("timetree", False)
         else "results/{build_name}/branch_lengths_no_time.json",
-        traits=rules.traits.output.node_data,
-        nt_muts=rules.ancestral.output.node_data,
-        aa_muts=rules.translate.output.node_data,
+        traits=build_dir + "/{build_name}/traits.json",
+        nt_muts=build_dir + "/{build_name}/nt_muts.json",
+        aa_muts=build_dir + "/{build_name}/aa_muts.json",
         clades=build_dir + "/{build_name}/clades.json",
-        mutation_context=rules.mutation_context.output.node_data,
-        recency=rules.recency.output.node_data if config.get("recency", False) else [],
-        colors=rules.colors.output.colors,
+        mutation_context=build_dir + "/{build_name}/mutation_context.json",
+        recency=build_dir + "/{build_name}/recency.json" if config.get("recency", False) else [],
+        colors=build_dir + "/{build_name}/colors.tsv",
         lat_longs=config["lat_longs"],
         description=config["description"],
         auspice_config=config["auspice_config"],

phylogenetic/rules/prepare_sequences.smk

@@ -83,7 +83,7 @@ rule filter:
 
 rule subsample:
     input:
-        metadata=rules.filter.output.metadata,
+        metadata=build_dir + "/{build_name}/good_metadata.tsv",
     output:
         strains=build_dir + "/{build_name}/{sample}_strains.txt",
         log=build_dir + "/{build_name}/{sample}_filter.log",
@@ -117,8 +117,8 @@ rule combine_samples:
             f"{build_dir}/{w.build_name}/{sample}_strains.txt"
             for sample in config["subsample"]
         ],
-        sequences=rules.filter.output.sequences,
-        metadata=rules.filter.output.metadata,
+        sequences=build_dir + "/{build_name}/good_sequences.fasta",
+        metadata=build_dir + "/{build_name}/good_metadata.tsv",
         include=config["include"],
     output:
         sequences=build_dir + "/{build_name}/filtered.fasta",
@@ -159,7 +159,7 @@ rule align:
       - filling gaps with N
     """
     input:
-        sequences=rules.reverse_reverse_complements.output,
+        sequences=build_dir + "/{build_name}/reversed.fasta",
         reference=config["reference"],
         genemap=config["genemap"],
     output: