ingest: Updates for augur curate and augur merge

[joverlee521]

Port changes from nextstrain/measles#52

[tsibley]

Since this repo is expected to be used to stamp out new repos, and we don't have any particular process/plan for how to update previously stamped out repos, I'm going to drop this bit of backwards compatibility that was in my measles implementation:

diff --git a/ingest/rules/nextclade.smk b/ingest/rules/nextclade.smk
index a70d994..41a2f75 100644
--- a/ingest/rules/nextclade.smk
+++ b/ingest/rules/nextclade.smk
@@ -18,6 +18,8 @@ See Nextclade docs for more details on usage, inputs, and outputs if you would
 like to customize the rules:
 https://docs.nextstrain.org/projects/nextclade/page/user/nextclade-cli.html
 """
+import sys
+
 DATASET_NAME = config["nextclade"]["dataset_name"]
 
 
@@ -61,6 +63,14 @@ rule run_nextclade:
         """
 
 
+if isinstance(config["nextclade"]["field_map"], str):
+    print(f"Converting config['nextclade']['field_map'] from TSV file ({config['nextclade']['field_map']}) to dictionary; "
+          f"consider putting the field map directly in the config file.", file=sys.stderr)
+
+    with open(config["nextclade"]["field_map"], "r") as f:
+        config["nextclade"]["field_map"] = dict(line.rstrip("\n").split("\t", 1) for line in f if not line.startswith("#"))
+
+
 rule join_metadata_and_nextclade:
     input:
         nextclade="results/nextclade.tsv",