Add abundance metrics

[d4straub]

This is a follow-up PR to #1023.

With this PR the comparison of observed to expected sequences is finished for now, I think. The results are not (yet) integrated to the pipeline summary report though.
A comparison of observed to expected taxa would be also great in future. Changing the test datasets to mock data could make the comparison also in tests meaningful.

This PR adds metrics based on abundances:

• pearson_cor: Pearson's Correlation (cor)
• spearman_rho: Spearman's Rank Correlation (rho)
• deviation: Median Percent Abundance Deviation
• mae: Mean Absolute Error (MAE)
• rmse: Root Mean Square Error (RMSE)
• ps: Proportional Similarity (PS)
• bray-curtis: Bray-Curtis Dissimilarity
• hellinger: Hellinger Distance
• jensen-shannon: Jensen-Shannon Divergence

and figures thereof, e.g.

and fixes a shortcoming in the previous PR that limited the blast result filtering.

Additionally, --expected_sequences_mismatches was added. It allows to increase the threshold for mismatches/gaps to call a TP. For example, --expected_sequences_mismatches 1 also allows observed sequences with 1 mismatch to an expected sequence to be accepted as TP (by default only exact matches, i.e. --expected_sequences_mismatches 0).

Previously, the comparison results were published in a folder that included the params md5sum in its path. While this was great for repeatedly resuming the pipeline with various parameters and accumulating all results in a single outdir directory, it proofed difficult: the CI tests seemed to not like missing files (md5sum changed when param was added) and md5sums were different between local & CI nf-test run due to differing parameter string. Therefore, the comparison results are now not published under a md5sum, but overwritten each time. The md5sum_version.txt still has all that info though.

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/ampliseq 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).

[erikrikarddaniel]

A few spelling mistakes.

[d4straub]

Thanks!