Nuclear contamination per library in MQC, plus fixes and cleanup of channels by james

[TCLamnidis]

1. Fixed deduplication output logic
2. Cleanup of channels that were not being used.
3. Updated parsing of nuclear contamination output to be compatible with latest version of angsd (0.933)
4. Nuclear contamination output per library now correctly shown in MQC report. Before, the nuclear contamination estimates were getting their own row in the general stats table because the process was written before the tuple input and inferred naming form filenames.

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 .).
• CHANGELOG.md is updated