fixed headers

README.md

@@ -38,7 +38,7 @@ lusSTR utilizes the ```lusstr``` command to invoke various Snakemake workflows.
 
 The ```lusstr snps``` command invokes the SNP analysis workflow. Please see below for further information on processing SNP data.
 ___
-### Creating the STR config file
+### Creating the SNP config file
 
 Running ```lusstr config``` creates a config file containing the default settings for the lusSTR STR analysis pipeline. The settings can be changed with command line arguments (see below) or by manually editing the config file. The default settings, along with their descriptions, are as follows:
 

lusSTR/cli/snps.py

@@ -1,31 +1,5 @@
 # -------------------------------------------------------------------------------------------------
-# Copyright (c) 2020, DHS.
-#
-# This file is part of lusSTR (http://github.com/bioforensics/lusSTR) and is licensed under
-# the BSD license: see LICENSE.txt.
-#
-# This software was prepared for the Department of Homeland Security (DHS) by the Battelle National
-# Biodefense Institute, LLC (BNBI) as part of contract HSHQDC-15-C-00064 to manage and operate the
-# National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and
-# Development Center.
-# -------------------------------------------------------------------------------------------------
-
-import lusSTR
-import snakemake
-
-## placeholder until I update this
-
-def main(args):
-    raise NotImplementedError('SNP workflow implementation pending')
-
-def subparser(subparsers):
-    p = subparsers.add_parser("snps", description="Running the entire STR pipeline (format, annotate and filter)")
-    p.add_argument("--config", default="config.yaml", help="config file used to identify settings.")
-    p.add_argument("-w", "--workdir", metavar="W", default=".", help="working directory")
-    p.add_argument("--skip-filter", dest="filter", action = "store_true", help="Skip filtering step")
-
-# -------------------------------------------------------------------------------------------------
-# Copyright (c) 2020, DHS.
+# Copyright (c) 2023, DHS.
 #
 # This file is part of lusSTR (http://github.com/bioforensics/lusSTR) and is licensed under
 # the BSD license: see LICENSE.txt.

lusSTR/wrappers/snps_convert.py

@@ -1,3 +1,15 @@
+# -------------------------------------------------------------------------------------------------
+# Copyright (c) 2023, DHS.
+#
+# This file is part of lusSTR (http://github.com/bioforensics/lusSTR) and is licensed under
+# the BSD license: see LICENSE.txt.
+#
+# This software was prepared for the Department of Homeland Security (DHS) by the Battelle National
+# Biodefense Institute, LLC (BNBI) as part of contract HSHQDC-15-C-00064 to manage and operate the
+# National Biodefense Analysis and Countermeasures Center (NBACC), a Federally Funded Research and
+# Development Center.
+# -------------------------------------------------------------------------------------------------
+
 import json
 import os
 import pandas as pd

lusSTR/wrappers/snps_format.py

@@ -1,5 +1,5 @@
 # -------------------------------------------------------------------------------------------------
-# Copyright (c) 2020, DHS.
+# Copyright (c) 2023, DHS.
 #
 # This file is part of lusSTR (http://github.com/bioforensics/lusSTR) and is licensed under
 # the BSD license: see LICENSE.txt.