Use nf-test in CI

[kbestak]

Adapted the CI script to run nf-test on files that have been changed.
Updated multiqc module.
Updated nftignore

Temporary fix - mindagap/duplicatefinder is missing the stub section - temporarily, the markedDups.txt is removed from testing.

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 - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/molkart branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• 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

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Hi @kbestak,

It looks like this pull-request is has been made against the kbestak/nf_molkart master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the kbestak/nf_molkart dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[FloWuenne]

Do we want a timestamp in the snapshot?!

[FloWuenne]

Looks good, just wanted you to confirm timestamp existence as wanted or not in the snapshots. Otherwise, feel free to merge @kbestak !

[FloWuenne]

LGTM 🚀 . Let's merge this and then do the template update @kbestak !

[kbestak]

The timestamp is included by defaut and it is just the snapshot's metadata, thanks for the review, I'll get the template update PR sorted out now.