initial draft for joss paper

Author: ntachukwu

paper/paper.bib

@@ -0,0 +1,29 @@
+@article{cwl: 2021,
+  	url = {https://arxiv.org/pdf/2105.07028.pdf},
+  	Archiveprefix = {arXiv},
+  	Author = {{Michael} R. C., {Peter} Amstutz,{Sanne} Abeln, {Alexandru} Iosup, {John} Chiltole, and the {CWL} community}
+  	Eprint = {arXiv:2105.07028v2},
+  	Journal = {ArXiv e-prints},
+  	Keywords = {Standazing Computational language, common workflow language},
+  	Month = Aug,
+  	Title = {{Method included: Standardizing Computational Reuse and Portability with the common workflow lanauge}},
+  	Year = 2021
+}
+
+@misc{wdl,
+  author = {WDL Community},
+  title = {Workflow Description Language (WDL)},
+  year = {2017},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/openwdl/wdl}
+}
+
+@misc{miniwdl,
+  author = {miniwdl Community},
+  title = {miniwdl},
+  year = {2018},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/chanzuckerberg/miniwdl/}
+}

paper/paper.md

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+---
+title: 'wdl2cwl: A Python tool for converting WDL workflow files to CWL workflows'
+tags:
+  - Python
+  - workflow
+  - workflow description language
+  - common workflow language
+  - Language
+date:  August 2022
+bibliography: paper.bib
+---
+
+# Summary
+
+Computational workflows are used in data analysis, enabling innovation and 
+decision-making in various fields of science. There are several competing workflow description languages, 
+WDL (Workflow description Language) and CWL (Common Workflow Languaage) are two examples
+of popularly used systems. WDL is a way to specify data processiing workflows with 
+a human-readable and writeable syntax. WDL makes it straightforward to define 
+complex analysis tasks, chain them together in workflows, and parallelize their execution [@wdl].
+CWL is a way to describe command line tools and connect 
+the together to create workflows. Because CWL is a specification and not a 
+specific piece of software, tools and workflows described using CWL are portable acroos
+a variety of platforms that support the CWL standard [@cwl:2021].
+
+It can be hard learning and adapting to the various knowledge requirements and
+specifications of a workflow language. This complication makes it hard for analysts and scientists 
+share their work and collaborate efficiently with others who are use to working with different language.
+
+``wdl2cwl`` is a Python package for converting workflow files written in WDL to workflows in CWL. Python
+allows flexibility and the ability to import other Python packages. 
+The ``wdl2cwl`` package uses the ``miniwdl`` package [@miniwdl], an open-source, Python package, 
+developer toolkit and local runner for running wdl files. The ``wdl2cwl`` package was
+designed to provide a class-based and developer-friendly interface for extracting 
+the various sections of a wdl file, dynamically create the various objects
+needed to create a valid cwl file ( this is done using the ``cwl.utils`` package [@cwl.utils], 
+an open-source, Python package for parsing cwl files) and performing error checking 
+for valid imports, input declarations, expressions etc.
+
+``wdl2cwl`` was designed to be used by both cwl and wdl professionals and researchers, as well
+students in courses on bioinformatics and data analytics. It has already been
+used to convert a number of wdl workflows. This tool makes it easier 
+to translate your favourite WDL workflows into CWL. This could be because of platform 
+dependency issues (like trying to reproduce a WDL workflow on a platform that only allows CWL),
+or it could be to eliminate the need for an anylyst who undersnd and writes CWL to learn WDL language
+in other to quickly use a WDL workflow or it could be to create a more widely available workflow
+that can be used by users of either languages and so much more.
+
+# Acknowledgements
+
+We acknowledge the work by tthe developers of miniwdl, cwl, wdl
+
+# References