hicar
nf-core/hicar
This pipeline analyses data for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.
Key tools
Run it
nfclaw run hicar --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/hicar/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run hicar --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
group | string | yes | matches ^\S+$ | |
replicate | integer | yes | ||
fastq_1 | string | yes | matches ^\S+\.f(ast)?q\.gz$ | |
fastq_2 | string | yes | ||
md5_1 | string | no | ||
md5_2 | string | no |
--input must match ^\S+\.csv$.
The samplesheet is a CSV with this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):
group,replicate,fastq_1,fastq_2Any of the optional columns above may be appended to the header when your data needs them: md5_1, md5_2.
From data files. --input may also be the data files — a directory (searched recursively), a quoted glob, or files (--input once per file) — from which nfclaw writes this samplesheet: fastq_1/fastq_2 from FastQ files (mates paired by _R1/_R2, or by _1/_2 when their read names show they are mates). Set the required columns no file determines with --sheet-set COLUMN=VALUE (a constant or a {sample}/{lane} template): group (matching ^\S+$); replicate (integer). 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:
nfclaw run hicar --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 = '!>=21.10.3'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run hicar ... --nxf-ver 21.10.3--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Nextflow 21.10.3 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
nfclaw run hicar --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.
group,replicate,fastq_1,fastq_2| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
group | string | required | matches ^\S+$ |
replicate | integer | required | — |
fastq_1 | string | required | matches ^\S+\.f(ast)?q\.gz$ |
fastq_2 | string | required | — |
md5_1 | string | optional | — |
md5_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
74 parameters · 11 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.
41 parameters · 33 hidden
MACS2 Peak Calling options5
read peak calling for fragment (R1) reads by MACS2
cutoff qvalue
cutoff pvalue for fragment (R1)
shift size for MACS2
extsize for MACS2
MAPS Peak Calling options8
resolution bin size
MAPS regression cutoff value
MAPS regression -log10(fdr) cutoff value
MAPS regression fold change cutoff value
output of restriction_cut_multipleenzyme.py.
MAPS regression filter file name
MAPS regression type
Type of snow cluster to use
Visualization options4
JVM heap parameters for juicer
The juicer_tools path
max events to plot for virtual 4c
create track files for virtual 4c or not
Experiment Config options2
Specifies that the cutting position has to be using.
Specifies that the cutoff value used for mappability filter.
Input Output options6
Path to anchor peaks
Email address for completion summary.
Path to comma-separated file containing information about the samples in the experiment.
Metho for 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.
Pipeline Controls6
skip trim 5'end TAC
skip differential analysis or not
skip enrichment or not
skip fastqc or not
skip multiqc or not
skip peak annotation or not
Reference Genome options10
Path to blacklist regions in BED format, used for filtering alignments.
Path to bwa index file.
Path to FASTA genome file.
Path to annotation gene bed file.
Name of iGenomes reference.
Path to annotation gff file.
Path to annotation gtf file.
Effective genome size parameter required by MACS2.
Path to genome mappability file.
UCSC assembly annotation name.
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/hicar/blob/1.0.0/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.