diff --git a/src/harpy/__main__.py b/src/harpy/__main__.py
index d5824ead5..c25fcfc40 100644
--- a/src/harpy/__main__.py
+++ b/src/harpy/__main__.py
@@ -30,6 +30,7 @@
 
 @click.group(options_metavar='', context_settings={"help_option_names" : ["-h", "--help"]})
 @click.version_option("0.0.0", prog_name="harpy")
+
 def cli():
     """
     An automated workflow for haplotagging linked-read data
diff --git a/src/harpy/snakefiles/containerize.smk b/src/harpy/snakefiles/containerize.smk
index 2aa6e42f6..53ee6fc30 100644
--- a/src/harpy/snakefiles/containerize.smk
+++ b/src/harpy/snakefiles/containerize.smk
@@ -6,7 +6,7 @@ onsuccess:
 
 rule all:
     input:
-        collect("{conda}.env", conda = ["qc","align","snp","sv","phase","r","simulations"])
+        collect("{conda}.env", conda = ["align", "phase", "qc", "r", "simulations", "snp", "stitch", "sv"])
 
 rule qc:
     output: "qc.env"
@@ -33,11 +33,16 @@ rule phase:
     conda: os.getcwd() + "/.harpy_envs/phase.yaml"
     shell: "touch {output}"
 
-rule r_env:
+rule r:
     output: "r.env"
     conda: os.getcwd() + "/.harpy_envs/r.yaml"
     shell: "touch {output}"
 
+rule stitch:
+    output: "stitch.env"
+    conda: os.getcwd() + "/.harpy_envs/stitch.yaml"
+    shell: "touch {output}"
+
 rule simulations:
     output: "simulations.env"
     conda: os.getcwd() + "/.harpy_envs/simulations.yaml"
diff --git a/src/harpy/validations.py b/src/harpy/validations.py
index 316b1d755..69fee37e8 100644
--- a/src/harpy/validations.py
+++ b/src/harpy/validations.py
@@ -18,7 +18,7 @@ def check_envdir(dirpath):
         print_error("This working directory does not contain the expected directory of conda environment definitions ([blue bold].harpy_envs/[/blue bold])\n  - use [green bold]--conda[/green bold] to recreate it")
         sys.exit(1)
     envlist = os.listdir(dirpath)
-    envs = ["qc", "align", "snp", "sv", "phase", "simulations", "r", "stitch"]
+    envs = ["align",  "phase", "qc", "r", "simulations", "snp", "stitch", "sv"]
     errcount = 0
     errtable = Table(show_footer=True, box=box.SIMPLE)
     errtable.add_column("File", justify="left", style="blue", no_wrap=True)