Use a rules folder for ingest to follow pathogen-repo-template

nextstrain · Jan 10, 2024 · f388525 · f388525
1 parent 3124b18
commit f388525
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Showing 6 changed files with 5 additions and 5 deletions.
diff --git a/ingest/Snakefile b/ingest/Snakefile
@@ -55,20 +55,20 @@ rule all:
         _get_all_targets,
 
 
-include: "workflow/snakemake_rules/fetch_sequences.smk"
-include: "workflow/snakemake_rules/transform.smk"
+include: "rules/fetch_sequences.smk"
+include: "rules/transform.smk"
 
 
 if config.get("upload", False):
 
-    include: "workflow/snakemake_rules/upload.smk"
+    include: "rules/upload.smk"
 
 
 if send_slack_notifications:
 
-    include: "workflow/snakemake_rules/slack_notifications.smk"
+    include: "rules/slack_notifications.smk"
 
 
 if config.get("trigger_rebuild", False):
 
-    include: "workflow/snakemake_rules/trigger_rebuild.smk"
+    include: "rules/trigger_rebuild.smk"
diff --git a/...kflow/snakemake_rules/fetch_sequences.smk → ingest/rules/fetch_sequences.smk b/...kflow/snakemake_rules/fetch_sequences.smk → ingest/rules/fetch_sequences.smk
diff --git a/...w/snakemake_rules/slack_notifications.smk → ingest/rules/slack_notifications.smk b/...w/snakemake_rules/slack_notifications.smk → ingest/rules/slack_notifications.smk
diff --git a/...st/workflow/snakemake_rules/transform.smk → ingest/rules/transform.smk b/...st/workflow/snakemake_rules/transform.smk → ingest/rules/transform.smk
diff --git a/...kflow/snakemake_rules/trigger_rebuild.smk → ingest/rules/trigger_rebuild.smk b/...kflow/snakemake_rules/trigger_rebuild.smk → ingest/rules/trigger_rebuild.smk
diff --git a/ingest/workflow/snakemake_rules/upload.smk → ingest/rules/upload.smk b/ingest/workflow/snakemake_rules/upload.smk → ingest/rules/upload.smk