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Adds MODKIT_LOCALIZE process to aggregate bedMethyl pileup counts localized around genomic features of interest (e.g. CpG islands), producing a TSV of percent-modification vs. offset from feature midpoints and an optional interactive HTML chart. Tests chain MODKIT_PILEUP -> TABIX_TABIX -> MODKIT_LOCALIZE using existing nf-core test-datasets (homo_sapiens nanopore BAM + genome.fasta.fai). Regions BED created inline; no new test data upload required. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Oxford Nanopore dorado basecaller module with automatic model selection, modified base calling (5mCG_5hmCG via combined model syntax), and optional alignment to a reference genome. Uses local SIF for Track 1 (lab use); Track 2 upstream blocked pending dorado bioconda package. Tests: 2 stub (CPU) + 2 real GPU tests (NVIDIA L40S, componc_gpu_batch). Uses --profile singularity,gpu to expose GPU via --nv flag. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Adds a stub test using the public HG002 GIAB pod5 from nf-core/test-datasets (PR nf-core/test-datasets#1968). Test references the file via modules_testdata_base_path so it resolves once that PR merges. Also commits the 2.2 MB 10-read pod5 subset locally for development. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Thin wrapper over nanoporetech/dorado:sha... adding version labels. Used by `wave freeze --dockerfile Dockerfile` to obtain a stable community.wave.seqera.io URI for nf-core upstream submission. See sandbox/TRACK2_wave_freeze.md for the full runbook. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
nf-core/parabricks modules use nvcr.io/nvidia/... directly without bioconda. Following same pattern: use nanoporetech/dorado:sha... from Docker Hub. Removes the singularity/docker ternary — single container field only. Local SIF override kept in tests/nextflow.config for MSKCC HPC testing. Tracking semantic version tags: nanoporetech/dorado#1584. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Container: sahuno/dorado:1.4.0 (wraps nanoporetech/dorado v1.4.0 + samtools) - meta.yml: document that dorado outputs SO:unknown; advise SAMTOOLS_SORT + SAMTOOLS_INDEX downstream (confirmed with GIAB HG002 10-read test on A100) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Composite visualization process for modkit localize results. Overlays multiple samples colored by condition with 3 smoothing options (loess, rolling_mean, binned). Produces PNG/PDF/SVG figures and combined TSVs. - main.nf: MODKIT_LOCALIZE_PLOT process using Seqera Wave R container - templates/plot_localize_composite.R: full R template with ggplot2 - environment.yml: r-base, r-data.table, r-ggplot2, r-zoo via conda-forge - meta.yml: documents inputs/outputs per nf-core convention - tests/: 4 nf-test cases (1 stub + 3 real: loess, rolling_mean, binned) - tests/data/: synthetic 2-sample TSVs + samplesheet for testing All 4 nf-tests pass with --profile conda. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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New module:
modkit/localizeTool
modkit — A bioinformatics tool for working with modified bases from Oxford Nanopore sequencing data.
What this module does
MODKIT_LOCALIZEaggregates bedMethyl pileup counts around genomic features of interest (e.g. CpG islands, gene bodies, repeat elements), producing:This enables investigation of modification enrichment or depletion patterns relative to genomic landmarks, analogous to a methylation profile around features.
Inputs
modkit pileup).faior.sizes)Outputs
*.tsv— percent-modification vs. offset table*.html— interactive chart*.log— debug logTests
Tests chain
MODKIT_PILEUP→TABIX_TABIX→MODKIT_LOCALIZEusing existing nf-core test-datasets (homo_sapiensnanopore BAM +genome.fasta.fai). Regions BED is created inline — no new test data upload required.nf-testpasses locally (singularity profile)nf-testpasses on SLURM compute node (job 17362918, 2 tests PASSED in 13s)nf-core modules lintpasses: 48/48 tests, 0 warnings, 0 failuresNotes
--regionsis required by the modkit 0.6.1 CLI (enforced at the tool level)modkit/pileupmodulemodkit/localize/plotsubmodule for composite multi-sample visualization is planned as a follow-up PR