Use metadata-only filtering for subsampling

Replaces FASTA outputs with strain list outputs for the subsample rule
such that sequence data are not inspected during most subsampling steps.
The exception to the rule are subsampling jobs that require a priority
score calculation that depends on the FASTA sequence of another
subsampled group. To handle this exception, we add a new rule to extract
just those subsampled sequences.

Finally, we collect subsampled sequences into a single deduplicated
FASTA output using augur filter's new interface with the `--exclude-all`
flag and multiple input support for `--include`.

Note that this commit also updates the conda environment to use a GitHub
branch instead of an official augur release.

workflow/snakemake_rules/main_workflow.smk

@@ -355,14 +355,12 @@ rule subsample:
          - priority: {params.priority_argument}
         """
     input:
-        sequences = _get_unified_alignment,
         metadata = _get_unified_metadata,
         sequence_index = rules.index_sequences.output.sequence_index,
         include = config["files"]["include"],
         priorities = get_priorities,
         exclude = config["files"]["exclude"]
     output:
-        sequences = "results/{build_name}/sample-{subsample}.fasta",
         strains="results/{build_name}/sample-{subsample}.txt",
     log:
         "logs/subsample_{build_name}_{subsample}.txt"
@@ -387,7 +385,6 @@ rule subsample:
     shell:
         """
         augur filter \
-            --sequences {input.sequences} \
             --metadata {input.metadata} \
             --sequence-index {input.sequence_index} \
             --include {input.include} \
@@ -403,7 +400,6 @@ rule subsample:
             {params.sequences_per_group} \
             {params.subsample_max_sequences} \
             {params.sampling_scheme} \
-            --output {output.sequences} \
             --output-strains {output.strains} 2>&1 | tee {log}
         """
 
@@ -468,10 +464,6 @@ def _get_subsampled_files(wildcards):
     ]
 
 rule combine_samples:
-    message:
-        """
-        Combine and deduplicate FASTAs
-        """
     input:
         sequences=_get_unified_alignment,
         sequence_index=rules.index_sequences.output.sequence_index,