From a458525d2ac3ea4193bc0b22a56eb94bfa748a23 Mon Sep 17 00:00:00 2001
From: Kim Andrews <17375001+kimandrews@users.noreply.github.com>
Date: Fri, 26 Jan 2024 15:15:02 -0800
Subject: [PATCH] Update top-level .gitignore Removed top-level .gitignore and
 replaced it with .gitignore from pathogen-repo-template:
 https://github.com/nextstrain/pathogen-repo-template/blob/cd1ef12987b71a1fd8dd73eafb8c8c4bd4e6d817/.gitignore

---
 .gitignore | 28 +++++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/.gitignore b/.gitignore
index b653f7d..7c37fa7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,18 +1,17 @@
-# Files created by the pipeline, which we want to keep out of git
-# (or at least out of _this_ git repo).
+# Files created by workflows that we usually want to keep out of git
+auspice/
+builds/
 data/
 results/
-auspice/
-build/
+logs/
+benchmarks/
 
 # Sensitive environment variables
 environment*
+env.d/
 
-# Snakemake state dir
-/.snakemake
-
-# Local config overrides
-/config_local.yaml
+# Snakemake
+.snakemake/
 
 # For Python #
 ##############
@@ -39,3 +38,14 @@ environment*
 Icon?
 ehthumbs.db
 Thumbs.db
+*~
+
+# IDE generated files #
+######################
+.vscode/
+
+# nohup output
+nohup.out
+
+# cluster logs
+slurm-*