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 processing workflows with 
+a human-readable and writable 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 pieces 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 workflows 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 can use a WDL workflow. It can be used to create a more 
+widely available workflow that can be used by analysts of either language.
+
+# Acknowledgements
+
+We acknowledge the Chan Zuckerberg Initiative (CZI) for supporting this work through their EOSS - Diversity & Inclusion grant. We are grateful to Outreachy and their internship program for organizing and providing support for two internships (six months) focused on building this project. Additionally, we acknowledge the work by the developers of miniwdl, CWL and WDL.
+
+# References