Epigenomicslatest-release

hic

nf-core/hic

Analysis of Chromosome Conformation Capture data (Hi-C)

version2.1.0fe4ac65631Jun 1, 2023 Upstream Usage docs

Key tools

FastQCMultiQC

Run it

nfclaw

nfclaw run hic --input samplesheet.csv --outdir results -profile docker

raw nextflow

nextflow run pipelines/hic/upstream -profile docker --input samplesheet.csv --outdir results

demo · bundled test profile

nfclaw run hic --demo --outdir results   # adds the upstream test profile (-profile test,docker)

Inputs

column	type	required	constraints
`sample`	string	yes	matches `^\S+$`
`fastq_1`	string	yes	matches `^\S+\.f(ast)?q\.gz$`
`fastq_2`	string	no

--input must match ^\S+\.csv$.

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):

csv

sample,fastq_1

Any of the optional columns above may be appended to the header when your data needs them: fastq_2.

From 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; fastq_1/fastq_2 from FastQ files (mates paired by _R1/_R2, or by _1/_2 when their read names show they are mates). Set other columns with --sheet-set COLUMN=VALUE. Preview it with --check; a run records it in <outdir>/provenance/ for replay.

Reference genome

No reference genome is set by default: supply your own reference. The schema declares AWS iGenomes at s3://ngi-igenomes/igenomes; selecting --genome <id> uses the paths in the pipeline's reference configuration. Access to that remote source is required. To supply your own reference, use e.g. --fasta; the reference_genome_options group in reference.md lists every reference option. Set --igenomes-ignore true to disable the lookup entirely. Confirm the selected reference's paths and source in the pinned upstream/nextflow.config and upstream/conf/ before running.

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:

bash

nfclaw run hic --input samplesheet.csv --outdir results -profile docker \
  --limit-cpus 4 --limit-memory 15.GB

nfclaw 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 = '!>=22.10.1'.

To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:

bash

nfclaw run hic ... --nxf-ver 22.10.1

--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.

Nextflow 22.10.1 predates process.resourceLimits (24.04.0), so --limit-* cannot be combined with this pin — nfclaw refuses it rather than run without the ceiling; cap resources with the release's own --max-cpus, --max-memory, --max-time instead.

Demo

bash

nfclaw run hic --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; optional columns from the table may be appended.

samplesheet.csv header

sample,fastq_1

Column	Type	Required	Allowed / constraints
`sample`	string	required	matches ^\S+$
`fastq_1`	string	required	matches ^\S+\.f(ast)?q\.gz$
`fastq_2`	string	optional	—

Required parameters

--inputstring (file path)

Path to comma-separated file containing information about the samples in the experiment.

Constraint · matches ^\S+\.csv$

--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

73 parameters · 12 groups

Every 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.

Groups

nextflow_schema.json

49 parameters · 24 hidden

Alignments6

Option for HiC-Pro end-to-end bowtie mapping

Option for HiC-Pro trimmed reads mapping

Read number per chunks if split_fastq is used

Keep aligned reads with a minimum quality value

Save all BAM files during two-steps mapping

Split the reads into chunks before running the pipelne

Contact Maps8

Resolution to build the maps (comma separated)

Generate raw and normalized contact maps with HiC-Pro

Threshold for HiC-Pro ICE convergence

Filter high counts rows before HiC-Pro normalization

Filter low counts rows before HiC-Pro normalization

Maximum number of iteraction for HiC-Pro ICE normalization

Maximum resolution to build mcool file

Save raw contact maps

Digestion Hi C6

Full path to file specifying chromosome sizes (tab separated with chromosome name and size)`.

Name of restriction enzyme to automatically set the restriction_site and ligation_site options (hindiii, mboi, dpnii, arima)

Expected motif after DNA ligation. Several motifs (comma separated) can be provided.

Full path to restriction fragment (bed) file.

Restriction motifs used during digestion. Several motifs (comma separated) can be provided.

If generated by the pipeline save the annotation and indexes in the results directory.

Dnase Hi C2

For Hi-C protocols which are not based on enzyme digestion such as DNase Hi-C

Minimum distance between loci to consider. Useful for --dnase mode to remove spurious ligation products. Only values > 0 are considered

Downstream Analysis4

Resolution for compartments calling

Resolution to build count/distance plot

Resolution to run TADs callers (comma separated)

Define methods for TADs calling

Generic options1

Custom MultiQC yaml file containing HTML including a methods description.

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.

Reference Genome options3

Full path to directory containing Bowtie index including base name. i.e. /path/to/index/base.

Path to FASTA genome file.

Name of iGenomes reference.

Skip options7

Do not run cooler balancing normalization

Do not run compartments calling

Do not run distance/decay plot

Do not build contact maps

Do not generate mcool file for Higlass visualization

Do not generate MultiQC report

Do not run TADs calling

Valid Pairs Detection8

Keep duplicated reads

Keep multi-aligned reads

Maximum fragment size to consider. Only values > 0 are considered

Maximum restriction fragment size to consider. Only values > 0 are considered

Minimum fragment size to consider. Only values > 0 are considered

Minimum restriction fragment size to consider. Only values > 0 are considered

Save a BAM file where all reads are flagged by their interaction classes

Save all types of non valid read pairs in distinct output files

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. --skip-multiqc true disables that report. 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/hic/blob/2.1.0/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.