diff --git a/ingest/Snakefile b/ingest/Snakefile
index 6411df9..f1d2404 100644
--- a/ingest/Snakefile
+++ b/ingest/Snakefile
@@ -22,9 +22,9 @@ wildcard_constraints:
 # TODO: Add link to centralized docs on standard Nextstrain metadata fields
 rule all:
     input:
-        sequences=expand("results/sequences_{segment}.fasta", segment=segments),
-        metadata=expand("results/metadata_{segment}.tsv", segment=segments),
-        metadata_all="results/metadata_all.tsv",
+        sequences=expand("results/{segment}/sequences.fasta", segment=segments),
+        metadata=expand("results/{segment}/metadata.tsv", segment=segments),
+        metadata_all="results/all/metadata.tsv",
 
 
 # Note that only PATHOGEN-level customizations should be added to these
@@ -40,10 +40,10 @@ rule create_final_metadata:
     input:
         metadata="data/subset_metadata.tsv"
     output:
-        metadata="results/metadata_all.tsv"
+        metadata="results/all/metadata.tsv"
     shell:
         """
-        mv {input.metadata} {output.metadata}
+        cp {input.metadata} {output.metadata}
         """
 
 # Allow users to import custom rules provided via the config.
diff --git a/ingest/build-configs/nextstrain-automation/config.yaml b/ingest/build-configs/nextstrain-automation/config.yaml
index 5c26ed0..0ebdc26 100644
--- a/ingest/build-configs/nextstrain-automation/config.yaml
+++ b/ingest/build-configs/nextstrain-automation/config.yaml
@@ -17,9 +17,9 @@ s3_dst: "s3://nextstrain-data/files/workflows/lassa"
 # Mapping of files to upload
 files_to_upload:
   ncbi.ndjson.zst: data/ncbi.ndjson
-  metadata_all.tsv.zst: results/metadata_all.tsv
-  sequences_all.fasta.zst: results/sequences_all.fasta
-  metadata_L.tsv.zst: results/metadata_L.tsv
-  sequences_L.fasta.zst: results/sequences_L.fasta
-  metadata_S.tsv.zst: results/metadata_S.tsv
-  sequences_S.fasta.zst: results/sequences_S.fasta
+  all/metadata.tsv.zst: results/all/metadata.tsv
+  all/sequences.fasta.zst: results/all/sequences.fasta
+  L/metadata.tsv.zst: results/L/metadata.tsv
+  L/sequences.fasta.zst: results/L/sequences.fasta
+  S/metadata.tsv.zst: results/S/metadata.tsv
+  S/sequences.fasta.zst: results/S/sequences.fasta
diff --git a/ingest/rules/curate.smk b/ingest/rules/curate.smk
index cf9fa92..29f2520 100644
--- a/ingest/rules/curate.smk
+++ b/ingest/rules/curate.smk
@@ -62,7 +62,7 @@ rule curate:
         annotations=config["curate"]["annotations"],
     output:
         metadata="data/all_metadata.tsv",
-        sequences="results/sequences_all.fasta",
+        sequences="results/all/sequences.fasta",
     log:
         "logs/curate.txt",
     benchmark:
@@ -121,11 +121,11 @@ rule subset_metadata:
     input:
         metadata="data/all_metadata.tsv",
     output:
-        subset_metadata="data/subset_metadata.tsv",
+        metadata="data/subset_metadata.tsv",
     params:
         metadata_fields=",".join(config["curate"]["metadata_columns"]),
     shell:
         """
         tsv-select -H -f {params.metadata_fields} \
-            {input.metadata} > {output.subset_metadata}
+            {input.metadata} > {output.metadata}
         """
diff --git a/ingest/rules/nextclade.smk b/ingest/rules/nextclade.smk
index d6595e5..fb044a2 100644
--- a/ingest/rules/nextclade.smk
+++ b/ingest/rules/nextclade.smk
@@ -5,12 +5,12 @@ and sequences to split the sequences into L and S segments.
 REQUIRED INPUTS:
 
     metadata    = data/subset_metadata.tsv
-    sequences   = results/sequences_all.fasta
+    sequences   = results/all/sequences.fasta
 
 OUTPUTS:
 
-    metadata        = results/metadata_{segment}.tsv
-    sequences       = results/sequences_{segment}.fasta
+    metadata        = results/{segment}/metadata.tsv
+    sequences       = results/{segment}/sequences.fasta
 
 See Nextclade docs for more details on usage, inputs, and outputs if you would
 like to customize the rules:
@@ -20,10 +20,10 @@ https://docs.nextstrain.org/projects/nextclade/page/user/nextclade-cli.html
 rule run_nextclade_to_identify_segment:
     input:
         metadata = "data/subset_metadata.tsv",
-        sequences = "results/sequences_all.fasta",
+        sequences = "results/all/sequences.fasta",
         segment_reference = config["nextclade"]["segment_reference"],
     output:
-        sequences = "results/sequences_{segment}.fasta",
+        sequences = "results/{segment}/sequences.fasta",
     params:
         min_seed_cover = config["nextclade"]["min_seed_cover"],
     shell:
@@ -38,10 +38,10 @@ rule run_nextclade_to_identify_segment:
 
 rule subset_metadata_by_segment:
     input:
-        metadata = "data/subset_metadata.tsv",
-        sequences = "results/sequences_{segment}.fasta",
+        metadata = "results/all/metadata.tsv",
+        sequences = "results/{segment}/sequences.fasta",
     output:
-        metadata = "results/metadata_{segment}.tsv",
+        metadata = "results/{segment}/metadata.tsv",
     params:
         strain_id_field = config["curate"]["output_id_field"],
     shell: