changes to allow include Snakefile
@@ -86,7 +86,7 @@ rule align:
- gaps relative to reference are considered real
"""
input:
- sequences = rules.filter.output.sequences,
+ sequences = "results/filtered.fasta",
reference = files.reference
output:
alignment = "results/aligned.fasta"
@@ -188,7 +188,7 @@ rule ancestral:
- not inferring ambiguous mutations
"""
input:
- tree = rules.refine.output.tree,
+ tree = "results/tree.nwk",
alignment = rules.mask.output
output:
node_data = "results/nt_muts.json"
@@ -207,7 +207,7 @@ rule ancestral:
rule translate:
message: "Translating amino acid sequences"
input:
- tree = rules.refine.output.tree,
+ tree = "results/tree.nwk",
node_data = rules.ancestral.output.node_data,
reference = files.reference
output:
@@ -228,7 +228,7 @@ rule traits:
- increase uncertainty of reconstruction by {params.sampling_bias_correction} to partially account for sampling bias
"""
input:
- tree = rules.refine.output.tree,
+ tree = "results/tree.nwk",
metadata = rules.download.output.metadata,
weights = files.weights
output:
@@ -251,7 +251,7 @@ rule traits:
rule clades:
message: "Adding internal clade labels"
input:
- tree = rules.refine.output.tree,
+ tree = "results/tree.nwk",
aa_muts = rules.translate.output.node_data,
nuc_muts = rules.ancestral.output.node_data,
clades = files.clades
