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DSL2 - CLASSIFY_MTDNA_HAPLOGROUP#1134

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trianglegrrl wants to merge 73 commits intodevfrom
dsl2-haplogrep3
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DSL2 - CLASSIFY_MTDNA_HAPLOGROUP#1134
trianglegrrl wants to merge 73 commits intodevfrom
dsl2-haplogrep3

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@trianglegrrl trianglegrrl commented May 1, 2025 •
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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).

@trianglegrrl trianglegrrl changed the base branch from master to dev May 1, 2025 13:31
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nf-core-bot commented May 1, 2025

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 trianglegrrl force-pushed the dsl2-haplogrep3 branch 4 times, most recently from 596e6d0 to 148ab55 Compare May 1, 2025 17:34
@trianglegrrl trianglegrrl changed the title VERY WIP for human mtdna haplogroup classification DSL2 - CLASSIFY_MTDNA_HAPLOGROUP May 1, 2025
@trianglegrrl trianglegrrl changed the title DSL2 - CLASSIFY_MTDNA_HAPLOGROUP DSL2 - [WIP] CLASSIFY_MTDNA_HAPLOGROUP May 1, 2025
trianglegrrl
trianglegrrl commented May 1, 2025
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subworkflows/local/classify_mtdna_haplogroup.nf
// https://github.com/nf-core/modules/tree/master/subworkflows
// You can also ask for help via your pull request or on the #subworkflows channel on the nf-core Slack workspace:
// https://nf-co.re/join
// TODO nf-core: A subworkflow SHOULD import at least two modules
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@trianglegrrl trianglegrrl May 1, 2025

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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.)

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@TCLamnidis TCLamnidis May 23, 2025

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

trianglegrrl
trianglegrrl commented May 1, 2025
View reviewed changes
workflows/eager.nf

if (params.run_mtdna_haplogroup) {
if (!params.run_genotyping) {
error "Cannot run mtDNA haplogroup classification (--run_mtdna_haplogroup) without running genotyping (--run_genotyping). VCF files are required as input."
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@trianglegrrl trianglegrrl May 1, 2025

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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.

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@TCLamnidis TCLamnidis May 23, 2025

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

@nf-core nf-core deleted a comment from github-actions bot May 1, 2025
@trianglegrrl trianglegrrl changed the title DSL2 - [WIP] CLASSIFY_MTDNA_HAPLOGROUP DSL2 - CLASSIFY_MTDNA_HAPLOGROUP May 2, 2025
TCLamnidis and others added 28 commits May 23, 2025 04:47
@TCLamnidis @VerbalCant
add command legend, and align a bit more
b81baee
@TCLamnidis @VerbalCant
Fix test. and snapshot.
c4dbdb9
@TCLamnidis @VerbalCant
bump nft-bam version
eb5b05a
@TCLamnidis @VerbalCant
Start over with new output directory structure
93b78cc
@TCLamnidis @VerbalCant
bump nft-bams to latest
f259820
@TCLamnidis @VerbalCant
remove premature snapshot
bc13a92
@TCLamnidis @VerbalCant
WIP test reimplementation
a2feb3e
@TCLamnidis @VerbalCant
add all remaining sections. tests still fail.
1372a10
@jfy133 @VerbalCant
Slightly improved docs phrasing and structure
56376e0
@jfy133 @VerbalCant
Add some TODOs
f7f2ccc
@jfy133 @VerbalCant
Add ebugging prints
9efc16a
@jfy133 @VerbalCant
Fix var name
289efda
@jfy133 @VerbalCant
Update test snapshot to exclude directories and contained files
072d57e
@jfy133 @VerbalCant
Add missing bam and flagstat files
11741b1
@TCLamnidis @VerbalCant
remove unused nft-bam plugin
f609d74
@TCLamnidis @VerbalCant
cleanup unused code and debug output
e20aa6a
@TCLamnidis @VerbalCant
add bamfiltering_savefilteredbams again
4b5be30
@TCLamnidis @VerbalCant
remve duplicate Qualimap config
781c16e
@TCLamnidis @VerbalCant
update test. add genotyping and metagenomics
787c0e2
@TCLamnidis @VerbalCant
update snapshot
fe0c6bc
@TCLamnidis @VerbalCant
exclude unstable files from md5sum
50df7f2
@TCLamnidis @VerbalCant
Stricter checking of VCF file checksums using nft-vcf.
ad2d0f7
@TCLamnidis @VerbalCant
add to unstable file list
99ef48b
@TCLamnidis @VerbalCant
better comments
3f7d22f
@TCLamnidis @VerbalCant
add 5p_misincorporation to ignore list
ada2f9d
@VerbalCant
Pass phylotree through to haplogrep3 module
22d22f4
@VerbalCant
Update testing docs with new params
b39f974
@TCLamnidis
Merge branch 'dev' into dsl2-haplogrep3
432bd67
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trianglegrrl commented May 23, 2025

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

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@trianglegrrl @nf-core-bot @TCLamnidis @VerbalCant @jfy133