diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..55cb325 --- /dev/null +++ b/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" diff --git a/README.md b/README.md index b845650..1ac77a0 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,13 @@ Logo +[![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. diff --git a/bin/Parameters.py b/bin/Parameters.py index ed8b458..1e0a106 100644 --- a/bin/Parameters.py +++ b/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}" + \