ingest: Move intermediate files to data directory

Follow up to review in the measles PR
nextstrain/measles#10 (comment)

ingest/Snakefile

@@ -47,7 +47,7 @@ else:
 
     rule create_final_metadata:
         input:
-            metadata="results/subset_metadata.tsv"
+            metadata="data/subset_metadata.tsv"
         output:
             metadata="results/metadata.tsv"
         shell:

ingest/rules/curate.smk

@@ -7,7 +7,7 @@ REQUIRED INPUTS:
 
 OUTPUTS:
 
-    metadata    = results/subset_metadata.tsv
+    metadata    = data/subset_metadata.tsv
     seuqences   = results/sequences.fasta
 
 """
@@ -61,7 +61,7 @@ rule curate:
         all_geolocation_rules="data/all-geolocation-rules.tsv",
         annotations=config["curate"]["annotations"],
     output:
-        metadata="results/all_metadata.tsv",
+        metadata="data/all_metadata.tsv",
         sequences="results/sequences.fasta",
     log:
         "logs/curate.txt",
@@ -118,9 +118,9 @@ rule curate:
 
 rule subset_metadata:
     input:
-        metadata="results/all_metadata.tsv",
+        metadata="data/all_metadata.tsv",
     output:
-        subset_metadata="results/subset_metadata.tsv",
+        subset_metadata="data/subset_metadata.tsv",
     params:
         metadata_fields=",".join(config["curate"]["metadata_columns"]),
     shell:

ingest/rules/nextclade.smk

@@ -4,7 +4,7 @@ and sequences.
 
 REQUIRED INPUTS:
 
-    metadata    = results/subset_metadata.tsv
+    metadata    = data/subset_metadata.tsv
     sequences   = results/sequences.fasta
 
 OUTPUTS:
@@ -64,7 +64,7 @@ rule run_nextclade:
 rule join_metadata_and_nextclade:
     input:
         nextclade="results/nextclade.tsv",
-        metadata="results/subset_metadata.tsv",
+        metadata="data/subset_metadata.tsv",
         nextclade_field_map=config["nextclade"]["field_map"],
     output:
         metadata="results/metadata.tsv",