From 3fb3e9e6d13bc9a7f2ecef567a674fdafd4166b7 Mon Sep 17 00:00:00 2001
From: Kim Andrews <17375001+kimandrews@users.noreply.github.com>
Date: Wed, 7 Feb 2024 17:05:58 -0800
Subject: [PATCH] Remove nextclade from Snakefile Remove nextclade-related
 if-else statements from Snakefile. This also requires editing final rule in
 curate.smk to output results/metadata.tsv instead of
 results/subset_metadata.tsv

---
 ingest/Snakefile        | 25 -------------------------
 ingest/rules/curate.smk |  2 +-
 2 files changed, 1 insertion(+), 26 deletions(-)

diff --git a/ingest/Snakefile b/ingest/Snakefile
index 65e8fca..41c316f 100644
--- a/ingest/Snakefile
+++ b/ingest/Snakefile
@@ -28,31 +28,6 @@ include: "rules/fetch_from_ncbi.smk"
 include: "rules/curate.smk"
 
 
-# We are pushing to standardize ingest workflows with Nextclade runs to include
-# Nextclade outputs in our publicly hosted data. However, if a Nextclade dataset
-# does not already exist, it requires curated data as input, so we are making
-# Nextclade steps optional here.
-#
-# If Nextclade config values are included, the nextclade rules will create the
-# final metadata TSV by joining the Nextclade output with the metadata.
-# If Nextclade configs are not included, we rename the subset metadata TSV
-# to the final metadata TSV.
-if "nextclade" in config:
-
-    include: "rules/nextclade.smk"
-
-else:
-
-    rule create_final_metadata:
-        input:
-            metadata="results/subset_metadata.tsv"
-        output:
-            metadata="results/metadata.tsv"
-        shell:
-            """
-            mv {input.metadata} {output.metadata}
-            """
-
 # Allow users to import custom rules provided via the config.
 # This allows users to run custom rules that can extend or override the workflow.
 # A concrete example of using custom rules is the extension of the workflow with
diff --git a/ingest/rules/curate.smk b/ingest/rules/curate.smk
index 9b0e37e..42b9b56 100644
--- a/ingest/rules/curate.smk
+++ b/ingest/rules/curate.smk
@@ -120,7 +120,7 @@ rule subset_metadata:
     input:
         metadata="results/all_metadata.tsv",
     output:
-        subset_metadata="results/subset_metadata.tsv",
+        subset_metadata="results/metadata.tsv",
     params:
         metadata_fields=",".join(config["curate"]["metadata_columns"]),
     shell: