Add Conda environment and use in most rules

Adds a Conda environment and references this environment in all rules
except the clean rule. The environment installs the Nextstrain base
package, providing all of the required dependencies to run the Zika
tutorial workflow.

This change allows this workflow to run with snk [1].

[1] https://snk.wytamma.com/

Author: huddlej

Snakefile

@@ -19,6 +19,7 @@ rule index_sequences:
         sequences = input_fasta
     output:
         sequence_index = "results/sequence_index.tsv"
+    conda: "envs/nextstrain.yaml"
     shell:
         """
         augur index \
@@ -45,6 +46,7 @@ rule filter:
         group_by = "country year month",
         sequences_per_group = 20,
         min_date = 2012
+    conda: "envs/nextstrain.yaml"
     shell:
         """
         augur filter \
@@ -69,6 +71,7 @@ rule align:
         reference = reference
     output:
         alignment = "results/aligned.fasta"
+    conda: "envs/nextstrain.yaml"
     shell:
         """
         augur align \
@@ -84,6 +87,7 @@ rule tree:
         alignment = rules.align.output.alignment
     output:
         tree = "results/tree_raw.nwk"
+    conda: "envs/nextstrain.yaml"
     shell:
         """
         augur tree \
@@ -111,6 +115,7 @@ rule refine:
         coalescent = "opt",
         date_inference = "marginal",
         clock_filter_iqd = 4
+    conda: "envs/nextstrain.yaml"
     shell:
         """
         augur refine \
@@ -135,6 +140,7 @@ rule ancestral:
         node_data = "results/nt_muts.json"
     params:
         inference = "joint"
+    conda: "envs/nextstrain.yaml"
     shell:
         """
         augur ancestral \
@@ -152,6 +158,7 @@ rule translate:
         reference = reference
     output:
         node_data = "results/aa_muts.json"
+    conda: "envs/nextstrain.yaml"
     shell:
         """
         augur translate \
@@ -170,6 +177,7 @@ rule traits:
         node_data = "results/traits.json",
     params:
         columns = "region country"
+    conda: "envs/nextstrain.yaml"
     shell:
         """
         augur traits \
@@ -194,6 +202,7 @@ rule export:
         auspice_config = auspice_config
     output:
         auspice_json = rules.all.input.auspice_json,
+    conda: "envs/nextstrain.yaml"
     shell:
         """
         augur export v2 \

envs/nextstrain.yaml

@@ -0,0 +1,5 @@
+name: nextstrain
+channels:
+  - nextstrain
+dependencies:
+  - nextstrain-base