[DSL2] Classify Human mtDNA Haplogroup

[trianglegrrl]

Work in progress - adding mtDNA haplogroup classification

Haplogrep3 integration

• --tree needs to be passed in from haplogrep3_tree_id
• should we be doing this from a consensus sequence vs vcf?
• verify RSRS support
• Get tests passing - add to humanpopgen ci.yml
• Filter VCF on MITOCHONDRIAL_NAME in SWF
• Update manual testing docs
• Test with full run (ancient0003, haplogrep3 web + CLI = "M32'56")

nextflow run main.nf -profile docker --input full_mito.csv --outdir ./results/ --run_genotyping --genotyping_tool ug --genotyping_source raw  --run_mtdna_haplogroup --fasta /references/mito/rCRS.fasta --fasta_fai /references/mito/rCRS.fasta.fai --skip_preprocessing --skip_damagecalculation --skip_qualimap -resume

[... 1h50m passes]

╰─ cat results/haplogrep3/ancient0003.txt
"SampleID"      "Haplogroup"    "Rank"  "Quality"       "Range"
"ancient0003"   "M32'56"        "1"     "0.9579"        "1-16569"

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/eager 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).