Add NGSCheckMate

[SPPearce]

This PR adds the NGSCheckMate tool to the pipeline. I find this an essential tool and part of my initial QC for all sequencing we perform. This tool takes a bed file with a set of SNPs and tries to determine if samples come from the same individuals. Developed and generally used in humans (there are SNP bed files for hg19/hg38/GRCh37/GRCh38 available), but could be used in other species if a suitable set of common SNPs was provided. This should be configured to run automatically on GRCh37/38, hg37/hg38 I think needs the files adding to igenomes - need to check.

This ensures that no sample swaps have occurred by checking:

• Replicates come from the same individual
• Paired samples (e.g. timepoints or tissue samples) come from the same individual
• Non-paired samples didn't come from the same individual! It works on human derived cell lines, but won't separate different treatments applied to the same cell line.

Testing. I have used a bed file on the test datasets to get it to run on yeast, haven't tried the full tests yet.

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• [ ] If you've fixed a bug or added code that should be tested, add tests!
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• [x] Usage Documentation in docs/usage.md is updated.
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