From f388525eb3ccf90b02d90b6da702425d3287209d Mon Sep 17 00:00:00 2001
From: Jennifer Chang <jennifer.chang.bioinform@gmail.com>
Date: Wed, 10 Jan 2024 15:20:31 -0800
Subject: [PATCH] Use a rules folder for ingest to follow
 pathogen-repo-template

---
 ingest/Snakefile                                       | 10 +++++-----
 .../snakemake_rules => rules}/fetch_sequences.smk      |  0
 .../snakemake_rules => rules}/slack_notifications.smk  |  0
 .../{workflow/snakemake_rules => rules}/transform.smk  |  0
 .../snakemake_rules => rules}/trigger_rebuild.smk      |  0
 ingest/{workflow/snakemake_rules => rules}/upload.smk  |  0
 6 files changed, 5 insertions(+), 5 deletions(-)
 rename ingest/{workflow/snakemake_rules => rules}/fetch_sequences.smk (100%)
 rename ingest/{workflow/snakemake_rules => rules}/slack_notifications.smk (100%)
 rename ingest/{workflow/snakemake_rules => rules}/transform.smk (100%)
 rename ingest/{workflow/snakemake_rules => rules}/trigger_rebuild.smk (100%)
 rename ingest/{workflow/snakemake_rules => rules}/upload.smk (100%)

diff --git a/ingest/Snakefile b/ingest/Snakefile
index 56848c4..453a327 100644
--- 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/ingest/workflow/snakemake_rules/fetch_sequences.smk b/ingest/rules/fetch_sequences.smk
similarity index 100%
rename from ingest/workflow/snakemake_rules/fetch_sequences.smk
rename to ingest/rules/fetch_sequences.smk
diff --git a/ingest/workflow/snakemake_rules/slack_notifications.smk b/ingest/rules/slack_notifications.smk
similarity index 100%
rename from ingest/workflow/snakemake_rules/slack_notifications.smk
rename to ingest/rules/slack_notifications.smk
diff --git a/ingest/workflow/snakemake_rules/transform.smk b/ingest/rules/transform.smk
similarity index 100%
rename from ingest/workflow/snakemake_rules/transform.smk
rename to ingest/rules/transform.smk
diff --git a/ingest/workflow/snakemake_rules/trigger_rebuild.smk b/ingest/rules/trigger_rebuild.smk
similarity index 100%
rename from ingest/workflow/snakemake_rules/trigger_rebuild.smk
rename to ingest/rules/trigger_rebuild.smk
diff --git a/ingest/workflow/snakemake_rules/upload.smk b/ingest/rules/upload.smk
similarity index 100%
rename from ingest/workflow/snakemake_rules/upload.smk
rename to ingest/rules/upload.smk