DSL2 - CLASSIFY_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
• 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).

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.0.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[trianglegrrl]

Is this true here? We don't really need more than one in this case, but it seems logical to have this as a subworkflow.

(The Y-DNA stuff will definitely offer making a reference genome that can be used by Yleaf as part of a subworkflow.)

[TCLamnidis]

Importing one one module is fine 👍
I agree that a SWF makes more sense.

[trianglegrrl]

So there used to be a vcf2genome in eager2 that output a consensus fasta. Is that still a thing? Because haplogrep3 also works with mtDNA sequences aligned to rCRS or RSRS.

[TCLamnidis]

no. vcf2genome is discontinued and will not be supported in eager 3.* .
Consensus sequence calling will be added soon™ ( #1142 ).

[trianglegrrl]

Whoops rebase disaster... See #1148 for proper commits