Patch getsoftwareversions java tools

[jfy133]

To close #885

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
  • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

This PR is against the master branch ❌

• Do not close this PR
• Click Edit and change the base to dev
• This CI test will remain failed until you push a new commit

---

Hi @jfy133,

It looks like this pull-request is has been made against the nf-core/eager master branch.
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[github-actions]

Markdown linting is failing

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[github-actions]

YAML linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

• Install yaml-lint
  • Install npm then install yaml-lint (npm install -g yaml-lint)
• Fix the markdown errors
  • Run the test locally: yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")
  • Fix any reported errors in your YAML files

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

[maxibor]

If the software_versions.csv file contains the correct software versions, that works for me !
(the get_software_versions process can not really fail)

[jfy133]

[patch-getsoftwraeversions-java](/nf-core/eager/tree/patch-getsoftwraeversions-java)

Will double check

[jfy133]

OK I'm having to update the eva config in tandem, and now mutlqic QC craps out. ugh

[jfy133]

Proof it now works. Also in tandem with a config update: nf-core/configs#382

[TCLamnidis]

LGTM