Paper

.github/workflows/draft-pdf.yml

@@ -0,0 +1,23 @@
+on: [push]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf

paper/paper.bib

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+@article{cwl,
+Author = {Michael R. Crusoe and Sanne Abeln and Alexandru Iosup and Peter Amstutz and John Chilton and Nebojša Tijanić and Hervé Ménager and Stian Soiland-Reyes and Bogdan Gavrilovic and Carole Goble and The CWL Community},
+Title = {Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language},
+Year = {2021},
+Eprint = {arXiv:2105.07028},
+Doi = {10.1145/3486897},
+}
+
+@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/}
+}
+
+@misc{cwl_utils,
+  author = {CWL Community},
+  title = {cwl-utils},
+  year = {2019},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/common-workflow-language/cwl-utils}
+}

paper/paper.md

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+---
+title: 'wdl2cwl: A Python tool for converting WDL workflows to CWL'
+tags:
+  - Python
+  - workflow
+  - workflow description language
+  - common workflow language
+authors:
+  - name: Dinithi Wickramaratne
+  - name: Dennis Chukwunta
+  - name: Michael R. Crusoe
+    orcid: 0000-0002-2961-9670
+  - name: Bruno P. Kinoshita
+    orcid: 0000-0001-8250-4074
+  - name: Peter Amstutz
+    orcid: 0000-0003-3566-7705
+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 systems,
+WDL (Workflow description Language) and CWL (Common Workflow Language) are two examples
+of popularly used systems. WDL offers 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 on the other hand, is a way to describe command line tools and connect 
+them together to create workflows. Because CWL is a specification and not a 
+specific piece of software, tools and workflows described using CWL are portable across
+a variety of platforms that support the CWL standard [@cwl].
+
+Groups using WDL or CWL can find it difficult to learn the other workflow definition
+language if they need to run their workflows in other platforms. It becomes even harder 
+when the workflows contain domain specific knowledge mixed with the definitions, and 
+when analysts and scientists need to consider future collaboration of other groups on 
+the workflows definitions.
+
+``wdl2cwl`` is a Python package for converting workflow written in WDL to workflows in CWL.
+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 and other useful operations on CWL files.
+
+``wdl2cwl`` was designed to be used by both CWL/WDL professionals and researchers, as well
+as students of bioinformatics and data analytics. It can help CWL analysts to avoid
+platform dependency issues (like trying to reproduce a WDL workflow on a platform that 
+only allows CWL). It can help analysts by eliminating the difficulty of learning a new
+workflow language before they an use a WDL worflow. It can be used to create a more 
+widely available workflow that can be used by analysts of either languages.
+
+# Acknowledgements
+
+We acknowledge the work by the developers of miniwdl, CWL and WDL.
+
+# References