Add script that runs parts of a single workflow with different files on different WES implementations

[mbarkley]

Motivation

A long-standing goal of the FASP GA4GH group has been to have a federated workflow demo that anyone can run. In this context, a federated workflow means:

1. Multiple compute environments are used for a single computational analysis
2. Different data is analysed in each compute environment
3. A single script drives the analysis using GA4GH standards, where possible

Goals

1. Automate as much of this task as possible in scripts in this repo
2. Use WES API to control and monitor workflows
3. Use public or synthetic data to make this more accessible for other people to try

Todo

• [ ] Identify some data (preferably with mirrors in different regions)
• [x] Fix script using DNAstack WES
• [x] Write script using ELIXIR WES
• [x] Write script using Seven Bridges WES
• [ ] Write single script calling DNAstack, WES, SB scripts on different subsets of files

[mbarkley]

There is a Seven Bridges WES script now thanks to #9

[ianfore]

Great proposal. I think there's even value in running something against more than one Seven Bridges implementation. I'd like to revive this model of looking at a FASP script to highlight which aspects of federation it hits. In this case it would address those in bold. It also has the option that we can test federated authentication and authorization early.

• Technology (stack)
• Funder
• Data provider
• National boundaries ?
• Scientific discipline

Your list above would check all those.

[ianfore]

Have updated FASPScript17 which runs a compute on TCGA and GTEx data in a single script. These come from different repositories and driver projects.

• [x] Create notebook version of FASPScript17
• [ ] Use DNAStack WES to run samtools workflow on GCP
• [x] Use Amazon copy of the GTEX data and run the workflow using the Seven Bridges CGC WES Client See FASPScript18 (script) and GTEXExample (notebook) which illustrate what would have to be added in 17 and the new notebook equivalent.

See GTEX_TCGA_Federated_Analysis notebook

[mbarkley]

There's now a PR sent to fix the DNAstack WES client. Tomorrow I'll start tinkering with an ELIXIR script.

[ianfore]

Merged the PR. Now thinking of tinkering with running samtools via the DNAStack WES. The problem we hit with that last summer seemed to be the "requester pays" buckets.

Added DNAStackWESTour notebook to explore some more.

It looks like we may still have the requester pays problem, but otherwise the server looks in good shape.

[mbarkley]

I've sent PR #19 with an ELIXIR WES client implementation. I don't think I'll get to write a script using all the WES clients this week for a single federated workflow, but I think we're a lot closer now.

[ianfore]

Raising the question whether the Federated VUS notebook addresses the intent of this issue. The link shown is the notebook that aggregates the results. Notebooks in the same folder show running the same workflow on three different instances of the Seven Bridges platform.

This...

1. Demonstrates the concept and checks the boxes in the 15 Jan 2021 comment above.
2. Is less convincing than running it on three different technical platforms

Barriers to the latter are

• Being able to access or deploy the application/container on Elixir or DNAStack
• Ability to get results back from those platforms when workflow is run

Proposing that we close this issue and address those barriers. Perhaps via issues in this repo which are specific to those barriers, or by other means.

Thoughts @mbarkley ?