updated Dockerfile, matched main.nf so that it can work with it

[subwaystation]

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
• If necessary, also make a PR on the nf-core/pangenome 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).

This PR fixes #36.

• Update Dockerfile
• Update the input parameters
• Update processes to work with the adjusted input parameters
• Add wfmash as alternative aligner
• Rename edyeet alignment parameters to alignment wherever possible
• Let the user decide which aligner to use, default is edyeet
• Write MAF output into the results folder
• Write SMOOTHED graph into the results folder
• Write all CONSENSUS graphs into the result folder
• Update file namings
• Update tests
• Integrate MultiQC
• Update help message
• Update README
• Escalate the publish-dir-mode argument.

[subwaystation]

Some tests are failing, because the current docker image is not checked out. Will correct.

[subwaystation]

@Zethson @heuermh I don't understand why the Markdown lintings are failing. The configuration file is set up in a way to ignore lines longer than 80 characters. I am confused.

[subwaystation]

@Zethson As discussed with @drpatelh I integrated a workaround until DavidAnson/markdownlint#373 is fixed. #47 is tracking this, too.

Else, all tests that should pass are passing :)

[Zethson]

LGTM