added citation information

CITATION.cff

@@ -0,0 +1,46 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Wirth
+  given-names: Joseph S.
+  orcid: "https://orcid.org/0000-0002-9750-2845"
+- family-names: Katz
+  given-names: Lee S.
+  orcid: "https://orcid.org/0000-0002-2533-9161"
+- family-names: Williams
+  given-names: Grant M.
+  orcid: "https://orcid.org/0000-0002-6033-485X"
+- family-names: Chen
+  given-names: Jessica C.
+  orcid: "https://orcid.org/0000-0002-9320-6774"
+doi: 10.5281/zenodo.13759569
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Wirth
+    given-names: Joseph S.
+    orcid: "https://orcid.org/0000-0002-9750-2845"
+  - family-names: Katz
+    given-names: Lee S.
+    orcid: "https://orcid.org/0000-0002-2533-9161"
+  - family-names: Williams
+    given-names: Grant M.
+    orcid: "https://orcid.org/0000-0002-6033-485X"
+  - family-names: Chen
+    given-names: Jessica C.
+    orcid: "https://orcid.org/0000-0002-9320-6774"
+  date-published: 2024-09-16
+  doi: 10.21105/joss.06850
+  issn: 2475-9066
+  issue: 101
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 6850
+  title: "primerForge: a Python program for identifying primer pairs
+    capable of distinguishing groups of genomes from each other"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.06850"
+  volume: 9
+title: "primerForge: a Python program for identifying primer pairs
+  capable of distinguishing groups of genomes from each other"

README.md

@@ -1,9 +1,13 @@
 <img src="assets/logo.png" alt="Logo" width="250" height="250">
 
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.06850/status.svg)](https://doi.org/10.21105/joss.06850)
+
 # primerForge
 
 software to identify primers that can be used to distinguish genomes
 
+If you use this software, please cite [our article](https://doi.org/10.21105/joss.06850) in the Journal of Open Source Software.
+
 ## Installation
 > [!NOTE]
 > `primerForge` is incompatible with versions python3.8 and below and python3.12 and above.

bin/Parameters.py

@@ -424,6 +424,8 @@ def printHelp():
             WIDTH = 21
             HELP_MSG = f"{EOL}Finds pairs of primers suitable for a group of input genomes{EOL}" + \
                        f"{GAP}{self.__author}, 2024{EOL*2}" + \
+                       f"If you use this software, please cite our article:{EOL}" + \
+                       f"{GAP}https://doi.org/10.21105/joss.06850{EOL*2}" + \
                        f"usage:{EOL}" + \
                        f"{GAP}primerForge [-{SHORT_OPTS.replace(':','')}]{EOL*2}" + \
                        f"required arguments:{EOL}" + \