methylong
nf-core/methylong
Extract methylation calls from long reads
Key tools
Run it
nfclaw run methylong --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/methylong/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run methylong --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
group | string | yes | matches ^\S+$ | |
sample | string | yes | matches ^\S+$ | |
path | string | yes | ||
ref | string (file path) | yes | matches ^\S+\.(fa|fasta|fna)(\.gz)?$ | |
method | string | yes | ont, pacbio |
The samplesheet is a CSV with this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):
group,sample,path,ref,methodFrom data files. --input may also be the data files — a directory (searched recursively), a quoted glob, or files (--input once per file) — from which nfclaw writes this samplesheet: sample from file names; ref from files matching their patterns, by sample name. Set the required columns no file determines with --sheet-set COLUMN=VALUE (a constant or a {sample}/{lane} template): group (matching ^\S+$); path (string); method (one of ont, pacbio). Preview it with --check; a run records it in <outdir>/provenance/ for replay.
Resources
Resource requests follow the pipeline's configs and selected profiles. nf-core's resource labels often assume a server — a single step can request far more memory than a workstation has, and retry rules can increase requests. If a run fails with Process requirement exceeds available memory (or CPUs), cap every request, and every retry, at what this machine actually has:
nfclaw run methylong --input samplesheet.csv --outdir results -profile docker \ --limit-cpus 4 --limit-memory 15.GBnfclaw turns those into Nextflow's process.resourceLimits and passes them as a -c config — the mechanism nf-core prescribes for exactly this (docs). Set them to the machine's real capacity. --limit-time DURATION also caps how long any one task may run: a task that needs longer is stopped, and so is every retry, so set it only as a deliberate ceiling, never as a guess at how long the analysis takes. The generated config is kept in <outdir>/provenance/, so commands.sh replays the run under the same ceiling.
Nextflow engine
This release declares nextflowVersion = '!>=25.04.0'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run methylong ... --nxf-ver 25.04.0--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run methylong --demo --outdir results # adds the upstream test profile (-profile test,docker)Samplesheet
A CSV with this header (the columns the schema requires). Fill each value per the constraints below.
group,sample,path,ref,method| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
group | string | required | matches ^\S+$ |
sample | string | required | matches ^\S+$ |
path | string | required | — |
ref | string (file path) | required | matches ^\S+\.(fa|fasta|fna)(\.gz)?$ |
method | string | required | ontpacbio |
Required parameters
--inputstring (file path)Path to comma-separated file containing information about the samples in the experiment.
--outdirstring (directory path)The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Parameter explorer
49 parameters · 10 groupsEvery parameter from the pinned nextflow_schema.json. nfclaw checks explicit values before launch; complex rules use the pinned pipeline's runtime validation. Search, filter by group, and expand any parameter for its default, allowed values and constraints.
31 parameters · 18 hidden
Alignment options2
Aligner option in ONT workflow, default is dorado aligner, specify minimap2 to switch
Aligner option in PacBio workflow, default is pbmm2, specify minimap2 to switch
Dmr options6
One of the group of DMR analysis in population scale
Another group of DMR analysis in population scale
Indicate if required DMR analysis for population scale
DMRer option in DMR analysis for haplotype level, default is dss, specify modkit to switch
DMRer option in DMR analysis for population scale, default is dss, specify modkit to switch
Indicate if to skip snvcall and phase
Fiberseq options1
Indicate if required m6a calling for fiberseq data
Input Output options4
Email address for completion summary.
Path to comma-separated file containing information about the samples in the experiment.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Mod Calling options6
Ccsmeth call freqb model.
Ccsmeth call mods model.
Specify dorado model, default is sup, other available models can be found on Dorado's GitHub repository.
Specify dorado modification, default is 5mC_5hmC, other available modifications can be found on Dorado's GitHub repository.
Indicate if required modcalling in PacBio workflow
Modcaller option in PacBio workflow, default is jasmine, specify ccsmeth to switch
Mod Pileup options6
Specify pileup context
Indicate if required bedgraphs as output
This option will identify and output all CG sites found in the consensus sequence from the reads in the pb-CpG-toolspileup (reference free); by default reference sequences are used to identify and output all CG sites.
Indicate if pileup m6a motif
Specify pbcpgtools pileup mode, default is using model mode, specify this parameter to switch to count mode
Pileup method in PacBio workflow, default is pbcpgtools, specify modkit to switch
Multiqc4
Display the help message.
Display the full detailed help message.
Custom MultiQC yaml file containing HTML including a methods description.
Display hidden parameters in the help message (only works when --help or --help_full are provided).
Preprocessing options2
Skip trimming in ONT workflow, will directly start from alignment step
Removes the alignment information added by aligners and updates flags accordingly
Outputs
Results land in --outdir; the files and directory layout depend on the selected workflow, parameters and publication settings. Run metadata is normally placed in <outdir>/pipeline_info/ (execution report, software versions), when those outputs are enabled. The pinned tree includes MultiQC support; a report is produced only when its workflow step runs. nfclaw run also writes <outdir>/provenance/ with the exact params file and the run log, <outdir>/provenance/logs/run.log — the whole launch, whose last line states the outcome (Nextflow's own log is <outdir>/.nextflow.log); unless --no-provenance it adds a run manifest (pinned version, commit and exact command), input/output SHA-256 checksums, and a replayable commands.sh.
The exact output files and directory layout for this release are documented upstream: github.com/nf-core/methylong/blob/2.0.0/docs/output.md
Check a run — in the foreground or the background — with nfclaw status <outdir>: success, still running, how it ended (with the error), or stopped without an outcome; exit 0 success, 3 running, 1 otherwise.