diff --git a/.gitignore b/.gitignore
index ccdcc60d4..348be3673 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,12 +3,14 @@
 test/
 src/
 .snakemake/
-Benchmark/
+.Benchmark/
+.harpy_envs/
 build/
 Demultiplex/
-Trim/
-Variants/
+QC/
+Align/
+SNP/
+SV/
 Impute/
 Phase/
-workflows/
-rules
\ No newline at end of file
+workflow/
\ No newline at end of file
diff --git a/Modules/impute.md b/Modules/impute.md
index ee08f70f3..1599698c7 100644
--- a/Modules/impute.md
+++ b/Modules/impute.md
@@ -26,7 +26,7 @@ curate your input VCF to meet criteria 3 and 4 prior to running the `impute` mod
 After variants have been called, you may want to impute missing genotypes to get the
 most from your data. Harpy uses `STITCH` to impute genotypes, a haplotype-based
 method that is linked-read aware. Imputing genotypes requires a variant call file 
-**containing SNPs**, such as that produced by `harpy variants`. You can impute genotypes with Harpy using the `impute` module:
+**containing SNPs**, such as that produced by `harpy snp`. You can impute genotypes with Harpy using the `impute` module:
 ```bash usage
 harpy impute OPTIONS... INPUTS...
 ```
diff --git a/Modules/phase.md b/Modules/phase.md
index 94b936d2d..3c2883b44 100644
--- a/Modules/phase.md
+++ b/Modules/phase.md
@@ -16,7 +16,7 @@ order: 2
 You may want to phase your genotypes into haplotypes, as haplotypes tend to be more informative
 than unphased genotypes (higher polymorphism, captures relationship between genotypes). Phasing
 genotypes into haplotypes requires alignment files, such as those produced by `harpy align` and
-a variant call file, such as those produced by `harpy variants` or `harpy impute`. **Phasing only
+a variant call file, such as those produced by `harpy snp` or `harpy impute`. **Phasing only
 works on SNP data**, and will not work for structural variants produced by `LEVIATHAN` or `NAIBR`. You can 
 phase genotypes into haplotypes with Harpy using the `phase` module: