This is a guest blog post from Anton Khodak, who was supported by the ongoing Open Bioinformatics Foundation travel fellowship program to attend a week long Common Workflow Language (CWL) workshop in London, November 2016. This was a natural continuation of Anton’s work on porting tools to the CWL as one of the OBF’s Google Summer of Code 2016 students.
The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences or workshops. The current call closes 15 April 2017 – if you’re planning to attend the OBF’s annual Bioinformatics Open Source Conference (BOSC) 2017 in Prague, you might want to apply?
After the successful completion of my GSoC projects, I had been invited to meet my mentors Michael R. Crusoe and Roman Valls Guimera for the CWL work session that took place in London from the 1st to the 4th of November, 2016. I was thrilled by this opportunity, and though it took quite a while for me to organize this journey (my first solo voyage abroad), it was undoubtfully worth it.
I arrived in London a little earlier to take part in Mozilla Festival 2016 together with Roman. At the festival, I presented my summer projects to people from the bioinformatics community who participated in Mozfest’s Open Science Fair.
The CWL week started a day later. The attendees were Michael (Common Workflow Language project), Roman (the Wolfson Wohl Cancer Research Centre), Janko Simonovic and Ivan Batic from Seven Bridges Genomics, Niels Drost from the Netherlands eScience Center, Robert Sugar from Intel Health and Life Sciences, and myself. During these four days, I worked on polishing the tools I developed (argparse2tool, pypi2cwl, cwl2argparse) on the basis of the feedback from all the participants. We explored the question of pip installability, filed a bunch of issues, tried applying argparse2tool to khmer scripts. Another thing we tackled was bug fixes for running Toil workflow engine on SLURM cluster. In addition, I learned about the inner workings of another important open-source implementation for CWL bunny directly from its creator Janko. During the CWL week, it was added to the community run continuous integration server and successfully passed the latest conformance tests.
Overall, it was a highly intensive and productive hackathon. I was very happy to meet my mentors and other people from the CWL community in person and to work with them for these few days. I could not imagine a better finish of my Google Summer of Code 2016 participation!
P.S. A year after, I became a mentor on a CWL project myself! Check the idea here: CWL reference implementation.
P.P.S. Special thanks to Open Bioinformatics Foundation for awarding me with the travel fellowship and reimbursing with that a significant part of my travel expenses.
(Above post contributed by Anton Khodak, originally on his blog, with our introduction added.)