Per sample genome sets

[erikrikarddaniel]

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/magmap 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).

This addresses issue #185 and adds the capacity to run mapping on sample-specific sets of genomes. The feature is only applied to remote genomes, not user-specified.

[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 @erikrikarddaniel,

It looks like this pull-request is has been made against the erikrikarddaniel/nf-core-magmap 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 erikrikarddaniel/nf-core-magmap 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!

[erikrikarddaniel]

@nf-core-bot fix linting

[erikrikarddaniel]

@danilodileo : This is ready for review. One test fails, but it's because it failed to fetch the container.

[danilodileo]

Great improvement!
I tried to re-run the test, let's see if it gets fixed

[danilodileo]

LGTM