Ash O'Farrell

Address log4j vulnerability in workflows

4

[Tag 4.2.4.0](https://github.com/broadinstitute/gatk/releases/tag/) doesn't appear to address the fact that WDLs still reference older GATK Docker images and therefore are still vulnerable. This is a quick replacement of all references to...

Use Docker image already on machine if present instead of always pulling from registries

2

Issues like #6827, hitting Docker Hub's stricter-as-of-late rate limits, or difficulty in developing a WDL with a private images could be all be bypassed if Cromwell were able to use...

Support forum link is dead -- is there any suitable replacement?

4

https://cromwell.readthedocs.io/en/stable/GettingHelp/ suggests that users get support at a forum that doesn't exist anymore. Normally when I find a dead link in docs, I just replace it in a PR, but...

Add support for ghcr.io Docker images

2

Cromwell doesn't support images from ghcr.io. Not sure if there's a workaround besides personally rehosting the image somewhere else. Seeing as a lot of bioinformatics images are hosted there I'd...

**Is your feature request related to a problem? Please describe.** Multi-workflow repos all default to the top-level README.md. This results in several issues: * The top-level README.md is scraped for...

Made a new ticket for this since it's a new issue. basename() does not work on optional values, but sometimes it seems to think things that aren't optional are optional....

GH branch-regex doesn't seem to work as expected with leading characters

1

**Describe the bug** As discussed in https://github.com/dockstore/dockstore-documentation/pull/229, we use this regex string when parsing branches from GitHub via the Dockstore GHA: `([a-zA-Z0-9]+([./_-]?[a-zA-Z0-9]+)*)$` My grasp of regular expressions is shaky at...

Dockstore entry markdown decides "this is a bullet point" differently from GitHub markdown

6

**Describe the bug** One of my [github-app workflows](https://dockstore.org/workflows/github.com/aofarrel/clockwork-wdl/clockwork_tuberculosis_example:main?tab=info) has a readme with bullet points and bold text. On GitHub the readme renders as expected, but on Dockstore a piece of...

Our handling of bad URLs doesn't provide information, can lead to infinite loop

2

Not sure if I should classify this as a bug or a feature request, feel free to modify as appropriate. **Describe the bug** We currently direct users to the Dockstore...

**Describe the bug** While trying to replicate #4437 with Charles, I realized that same repo has a different ghost workflow. (I'm using ghost to mean "a workflow with no descriptor...