Configuration¶

A run is config/config-base.yml (every key, with its default and a comment) plus a project config passed with --configfile, deep-merged over it. A project config states only what differs.

pixi run run-bodhi --configfile config/my-project.yml
pixi run snakemake -n --configfile config/my-project.yml            # dry run
pixi run list-models --configfile config/my-project.yml

Two project configs can be layered (--configfile a.yml b.yml); later files win key by key.

Keys¶

Inputs and outputs¶

Key	Default	Notes
`samples`	`config/samples.tsv`	see Samples file
`output_directory`	`results`	everything is written under here; Alpine: on `/scratch/alpine`
`reference.fasta`	`null`	genome FASTA, plain or bgzipped; required unless every sample overrides it
`reference.preset`	`lr:hq`	minimap2 preset for the index and alignment

dorado¶

Key	Default	Notes
`dorado.version`	`"2.1.2"`	the release `pixi run setup` installs
`dorado.device`	`cuda:all`	every GPU in the allocation
`dorado.emit_moves`	`true`	keep the `mv` move table (needed by signal-level tools; ~2× BAM size)
`dorado.min_qscore`	`0`	drop reads below this mean Q at basecall time
`dorado.trim`	`all`	`all`, `adapters`, `none`
`dorado.barcode_both_ends`	`false`	barcoded runs only
`dorado.resume`	`true`	keep `<bam>.partial` and pass `--resume-from` on retry
`dorado.extra_opts`	`""`	anything else, verbatim

models¶

See Models.

Key	Default
`models.directory`	`resources/models`
`models.simplex`	`dna_r10.4.1_e8.2_400bps_sup@v5.2.0`
`models.modified_bases`	`[5mC_5hmC, 6mA]`
`models.custom`	`[]`
`models.mod_versions`	pinned versions per simplex model

minknow¶

Key	Default	Notes
`minknow.include_fail`	`false`	for `basecalled: true` runs, also collect `bam_fail` / `pod5_fail`

align¶

Key	Default	Notes
`align.tool`	`dorado`	`dorado` (dorado aligner, keeps every tag) or `minimap2` (`samtools fastq -T '*'` → `minimap2 -y`)
`align.mm2_opts`	`""`	extra minimap2 options
`align.exclude_flags`	`0x904`	`samtools view -F`: unmapped, secondary, supplementary
`align.min_mapq`	`0`	`samtools view -q`

modkit¶

Key	Default	Notes
`modkit.pileup`	`true`	bedMethyl per sample
`modkit.filter_threshold`	`null`	pass threshold; null = modkit's estimate
`modkit.mod_thresholds`	`{}`	e.g. `{m: 0.8, a: 0.9}`
`modkit.cpg`	`false`	CpG sites only (`--cpg`)
`modkit.combine_strands`	`false`	with `cpg` or a motif
`modkit.motifs`	`[]`	`["GATC,1"]` → `--motif GATC 1`
`modkit.extra_opts`	`""`
`modkit.summary`	`true`	`modkit summary --tsv`
`modkit.extract_calls`	`false`	per-read, per-site calls (large)
`modkit.bigwig`	`false`	one bigWig of fraction modified per mod code
`dmr.contrasts`	`[]`	`[{name, a, b, base}]` → `modkit dmr pair`

qc¶

Key	Default
`qc.mosdepth`	`true`
`qc.read_summary`	`true` (dorado summary per read)

dnascent¶

See DNAscent. enabled, version, sif, command, singularity_bind, singularity_setup, gpu, min_mapq, min_length, per_read_probs, forksense.{enabled, order, opts}.

custom¶

See Custom steps.

Housekeeping¶

Key	Default	Notes
`cleanup_intermediates`	`false`	`true` or a list of tiers (`basecall`, `demux`) to `temp()` during the run
`escpod_version`	`"0.20.0"`	POD5 tooling used by `make-test-data`

pixi run clean --configfile <project.yml> is the on-demand superset: it removes pod5/ links, bam/basecall, bam/basecall_run, demux/ and bam/aligned, keeping bam/final, summary/, reference/, dnascent/.