Added nuclear_contamination to MultiQC report as custom content.

[TCLamnidis]

Various changes:

• Added latest version of Sex.DetERmine to environment.yaml. This version doesn't fail horribly when a bin has 0 coverage, instead setting the rates to 0.
• Removed second barplot (snp_counts) from multiqc_report. Not that useful, but easier to hide it than to change MQC modules.

Nuclear_contamination changes:

• Added nuclear contamination JSON output into multiQC
• Order of columns fixed so they come after SexDet.

To Do:

• Hide non default columns from nuclear_contamination output.
• SampleID is not correctly assigned in some cases. When running with -profile test_tsv_humanbam, library entry is correctly assigned,but individual level entry has _rmdup added to Sample ID in the JSON. Looking into it.

PR checklist

• This comment contains a description of changes (with reason)
• Ensure the test suite passes (nextflow run . -profile test,docker --paired_end).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated

[TCLamnidis]

PR into docs-updates so the nuclear_contamination columns are added without conflicts.

Issues:
#504