Michael Franklin

Optional inputs for DSL2

18

## New feature Pinging @rsuchecki @pditommaso (I couldn't find an issue with this, I hope it's okay that I open a new one). Based on a small conversation on the...

Disable digest lookup

8

Reopening https://github.com/broadinstitute/cromwell/pull/5545 as an internal branch so tests run correctly. Changelog: - Added config option `docker.perform-registry-lookup-if-digest-is-provided` with default True (https://github.com/broadinstitute/cromwell/pull/5545/commits/e9965d8f9a385b289f15b23b3fb923ecb8c0ea38) - Added logic to `DockerConfiguration.scala` to `sendDockerRequest` if `performRegistryLookupIfDigestIsProvided` is...

AWS S3: Can't access data outside my region (Status Code: 301)

3

Hi! I'm having some trouble request s3 objects that are outside my current region (I get a Status Code: 301). Backend: AWS Batch Filesystem: S3 Region : `ap-southeast-2` I'm attempting...

Add ability to manipulate WorkflowOutputParameter with some valueFrom

1

Per discussion in the [2020-09-29 CWL community chat](https://docs.google.com/document/d/1xeHTMVMh2xTssKg-IInbqaNwMtQGeVu_zQu5ffuzvrs/edit?ts=5f734348), it would be useful for me to perform some JavaScript expression on the output from some step. As also mentioned, it would...

File Bundles and Secondary / Accessory Files

21

Dear WDL team! I was hoping to source the community opinion on file bundles, or CWL's secondary files. This issue was spawned from: https://github.com/broadinstitute/cromwell/issues/2269 and also within the [WDL forum](https://gatkforums.broadinstitute.org/wdl/discussion/9299/secondary-index-files-and-directories-in-wdl)...

Clarifying "Absence of presence" and "presence of absence" (optional -> non optional task input with default)

13

Essentially, if I have some workflow and task that connections an optional value to a non-optional value. This should be a validation failure right? ```wdl workflow SmallWorkflow { input {...

Different VCF conventions

1

Is there a document or good summary of the different types / conventions for VCF? For example, VCF, sites-only VCF, gVCF, pVCF, spVCF. EG: - A gVCF (Genomic VCF) contains...

[batch] Add resource_usage endpoint for jobs

3

Hi! I know this is out of the blue, but we would like the ability to fetch resource_usage data from an endpoint programmatically to evaluate our job performance. I thought...

### What happened? Based on conversation: https://hail.zulipchat.com/#narrow/stream/223457-Hail-Batch-support/topic/Cancelling.20audit.20trail/near/408632944 (I hope the format of the title is okay, I'm gently requesting this functionality). ### Version 0.2.126-01714cc51f09 ### Relevant log output _No response_

Can the parsers avoid building full URLs

2

Trying to parse the outputSource of a workflow: ```cwl outputs: - id: out type: File outputSource: hello/out ``` But the output source gets resolved to: ``` 'file:///Users/franklinmichael/source/janis-core/ingestion/workflow/hello_v1_0_0.cwl#hello/out/hello/out' ``` I don't...