feat: add holodeck modules (simulate, mutate, methylate, eval)#12176
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atrigila
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Jul 2, 2026
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| "##fileformat=VCFv4.4", | ||
| "##holodeckVersion=0.3.0", | ||
| "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">", | ||
| "##FORMAT=<ID=MT,Number=.,Type=String,Description=\"Methylation state, top strand. Per-haplotype pipe-separated bitstring: 1=methylated, 0=unmethylated, .=haplotype carries REF or no owned CpG.\">", | ||
| "##FORMAT=<ID=MB,Number=.,Type=String,Description=\"Methylation state, bottom strand. Per-haplotype pipe-separated bitstring: 1=methylated, 0=unmethylated, .=haplotype carries REF or no owned CpG.\">", | ||
| "##contig=<ID=MT192765.1,length=29829>", | ||
| "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tMETHYLATE", | ||
| "MT192765.1\t37\t.\tC\t.\t.\t.\t.\tMT:MB\t0|0:0|0", | ||
| "MT192765.1\t64\t.\tC\t.\t.\t.\t.\tMT:MB\t0|0:0|0", |
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This block is the decompressed VCF body — one record per CpG site with the simulated methylation state (MT/MB FORMAT) — which is deterministic for a fixed input, so it snapshots stably. I've now also filtered the ##holodeckVersion header line (alongside ##holodeckCommand) so the snapshot won't churn on holodeck releases. Happy to adjust if you had a different concern in mind.
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Add an nf-core module wrapping `holodeck simulate`. Simulate sequencing reads from a reference genome. Emits paired-end FastQ plus optional ground-truth golden BAM/VCF, with an optional VCF input to embed variants into the reads. holodeck is a modern NGS read simulator written in Rust. The module is tested against the sarscov2 reference and includes a stub run.
Add an nf-core module wrapping `holodeck mutate`. Generate a VCF of random mutations from a reference genome. holodeck is a modern NGS read simulator written in Rust. The module is tested against the sarscov2 reference and includes a stub run.
Add an nf-core module wrapping `holodeck methylate`. Generate a methylation-annotated VCF (MT/MB FORMAT fields) from a reference genome, optionally annotating an input VCF of phased variants. holodeck is a modern NGS read simulator written in Rust. The module is tested against the sarscov2 reference and includes a stub run.
Add an nf-core module wrapping `holodeck eval`. Evaluate alignment placement accuracy of holodeck-simulated reads, comparing mapped positions against the simulated truth (golden BAM or encoded read names). holodeck is a modern NGS read simulator written in Rust. The module is tested against the sarscov2 reference and includes a stub run.
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@atrigila thanks for suggestions, any chance you can take another look? |
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Thanks for addressing the comments
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Description
Adds four new modules for holodeck, a modern NGS read simulator written in Rust:
holodeck/simulate— simulate paired-end reads from a reference (optional variants VCF, optional ground-truth golden BAM/VCF).holodeck/mutate— generate a VCF of random mutations from a reference.holodeck/methylate— generate a methylation-annotated VCF (MT/MB FORMAT fields).holodeck/eval— evaluate alignment placement accuracy of simulated reads.All tested against the sarscov2 reference with stub runs.
PR checklist
label.bioconda::holodeck=0.3.0; Seqera Wave community containers).nf-core modules test holodeck/<sub> --profile dockerpasses for all four.topic: versions.