diff --git a/.gitignore b/.gitignore
index ef13b00..a280ae4 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,40 +1,25 @@
-# Files created by the pipeline, which we want to keep out of git
-# (or at least out of _this_ git repo).
+# pipeline output #
+benchmarks/
 data/
+logs/
 results/
-build/
 
-# Sensitive environment variables
-environment*
-
-# Snakemake state dir
-/.snakemake
-
-# Local config overrides
-/config_local.yaml
+# snakemake output #
+.snakemake
+snakemake_log
 
 # For Python #
-##############
 *.pyc
 .tox/
 .cache/
-
-# Compiled source #
-###################
-*.com
-*.class
-*.dll
-*.exe
-*.o
-*.so
+__pycache__/*
 
 # OS generated files #
-######################
 .DS_Store
-.DS_Store?
 ._*
 .Spotlight-V100
 .Trashes
 Icon?
 ehthumbs.db
 Thumbs.db
+*~