Paper: Orchestrating Bioinformatics Workflows Across a Heterogeneous Toolset with Flyte

[pryce-turner]

Hello!

I didn't realize the review process started so early; this submission had to compete with a number of other high-priority items. As such, this is an incomplete first draft and I ask that reviewers kindly afford me some more time to clean it up before investing time reviewing it. I will adjust the PR title and contact relevant parties at that time.

Thank you for your patience and understanding!

Editor: Chris Calloway @cbcunc

Reviewers:

• Andrew James @Amjames
• Dr Kirtan Dave @davekits

[hongsupshin]

@pryce-turner Hi there, could you provide us with a timeline on when you can get the draft ready for the review?

[cbcunc]

@pryce-turner Is this still a "draft in progress?" If not, please remove draft from the PR title. If so, we only accept complete drafts for submission. We need to assign reviewers and don't wish to assign reviewers to a paper that is not complete. Please indicate that the paper is ready for review.

[github-actions[bot]]

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[pryce-turner]

Hi @hongsupshin and @cbcunc, this is now ready for review. Thanks for your patience!

[cbcunc]

Review reminders sent to @amjames and @davekits

[pryce-turner]

@amjames thank you so much for the thorough review! I think things are a lot clearer now but am of course always open to further suggestions.

[davekits]

My name is Kirtan, and I am one of the paper's reviewers.I will work on reviewing the paper and offering feedback.

[davekits]

@pryce-turner The aligners utilize indexes to map reads, and it is crucial to have a comprehensive discussion on the mechanism and parameters of aligners, particularly for single-end and paired-end data types.Additionally, the method does not include the development of a VCF file, which is necessary for variant analysis.

[pryce-turner]

Thanks for the comments @davekits! Despite alignment being a massive topic, I agree that a slightly more in-depth discussion, especially around the role of the index, is warranted. I'll avoid going too much into the weeds of dynamic programming or global vs local though, for example. A similarly detailed investigation of variant calling would likely be beneficial. This will be a fair bit more work since I have to develop the actual tasks and update the workflow behind the paper before I can discuss them. I'll focus on the presentation for now since this example adequately motivates the discussion around different tools playing nicely together; I'll focus on your suggested edits next week!