Outputs¶

Everything lands under output_directory. <s> is a sample id.

Per sample¶

Path	Rule	Content
`bam/final/<s>/<s>.bam`, `.bai`	`finalize_bam`	aligned, coordinate-sorted, primary alignments only (`align.exclude_flags`); dorado's `MM`/`ML` modbase tags, `mv` move table, `RG` and per-read tags all preserved
`summary/modkit/<s>/<s>.pileup.bed.gz`, `.tbi`	`modkit_pileup`	bedMethyl (below)
`summary/modkit/<s>/<s>.modkit_summary.tsv`	`modkit_summary`	per mod code: pass threshold, fraction modified over a read sample
`summary/modkit/<s>/<s>.mod_calls.tsv.gz`	`modkit_extract_calls` (opt)	one row per read per called site
`summary/modkit/<s>/<s>.<code>.bw`	`modkit_bigwig` (opt)	fraction modified per site, one file per mod code
`summary/qc/<s>/<s>.flagstat.tsv`	`samtools_qc`	`samtools flagstat -O tsv`
`summary/qc/<s>/<s>.stats.txt`	`samtools_qc`	`samtools stats`
`summary/qc/<s>/<s>.mosdepth.summary.txt`, `.mosdepth.global.dist.txt`	`mosdepth`	depth per contig, cumulative depth distribution
`summary/tables/<s>/<s>.read_summary.tsv.gz`	`dorado_read_summary`	`dorado summary`: per read length, mean qscore, alignment fields
`summary/custom/<step>/<s>/`	`custom_sample_step`	whatever the step declared
`dnascent/<s>/...`	DNAscent rules	see DNAscent

Intermediates (removed by pixi run clean):

Path	Content
`pod5/samples/<s>/pod5/`, `pod5_files.txt`	links to the input POD5 and a manifest of real paths
`pod5/runs/<run>/...`	same, per barcoded run
`bam/basecall/<s>/<s>.bam`	dorado's unaligned output (or MinKNOW's, concatenated)
`bam/basecall_run/<run>/<run>.bam`, `demux/<run>/`	barcoded runs: the run basecall and its demux
`bam/aligned/<s>/<s>.bam`	the aligned BAM `bam/final` hardlinks

Path	Content
`summary/samples_summary.tsv`	one row per sample: total/primary/mapped reads, mapped fraction, mean depth, read N50 and mean length, mean qscore, total bases, `modkit_<base>_<code>_pass_frac` per mod code
`summary/dmr/<contrast>.dmr.bed`	`modkit dmr pair` output per `dmr.contrasts` entry
`summary/custom/<step>/project/`	project-scoped custom steps
`reference/<name>-<hash>/genome.fa`, `.fai`, `.mmi`, `genome.chrom.sizes`	the staged reference and its indexes
`manifest.json`	git commit/branch/dirty flag, the merged config, the resolved model stack with paths, sample inputs, tool versions, host, user, start/end time, status
`logs/<rule>/...`	tool logs

modkit pileup writes the bedMethyl described in the modkit README. The columns that matter most:

Column	Meaning
1–3	chrom, start, end (0-based, half-open, one base)
4	mod code: `m` 5mC, `h` 5hmC, `a` 6mA, `21839` 4mC
5	valid coverage (score column)
6	strand (`+`/`-`; `.` when strands are combined)
10	N valid coverage
11	fraction modified, 0–100
12–18	N mod, N canonical, N other mod, N delete, N fail, N diff, N no-call

With modkit.cpg: true and combine_strands: true, the two strands of each CpG are one row.

Path	Content
`dnascent/<s>/index.dnascent`	read id → POD5 map
`dnascent/<s>/<s>.detect.bam`	detect output: `MM:Z:N+b?` (BrdU) / `N+e?` (EdU), `ML` = round(p·255)
`dnascent/<s>/<s>.detect.sorted.bam`, `.bai`	sorted, indexed copy
`dnascent/<s>/<s>.per_read.tsv.gz`	per read: n calls, mean and fraction-above-threshold for BrdU and EdU
`dnascent/<s>/forksense/<s>.forkSense` + `*_DNAscent_forkSense.bed`	forkSense calls: origins, terminations, left/right forks, analogue tracks, stress signatures