Define where the pipeline should find input data and save output data.

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

required
type: string
pattern: ^\S+\.(csv|tsv|yaml)$

Metho for the experiment.

type: string
default: HiCAR

Path to anchor peaks

type: string
pattern: ^\S+\.(narrowPeak|boradPeak)$

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

required
type: string

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

type: string

Path to FASTA genome file.

type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

Directory / URL base for iGenomes references.

hidden
type: string
default: s3://ngi-igenomes/igenomes

Do not load the iGenomes reference config.

hidden
type: boolean

Path to bwa index file.

type: string

Path to annotation gtf file.

type: string

Path to annotation gff file.

type: string

Path to annotation gene bed file.

type: string

Path to genome mappability file.

type: string

Effective genome size parameter required by MACS2.

type: string

UCSC assembly annotation name.

type: string

Path to blacklist regions in BED format, used for filtering alignments.

type: string

publish mappability to results genome/mappability folder

type: boolean

publish genome

type: boolean

Parameters used to describe the experiment designs.

Specifies that the cutting position has to be using.

type: string
default: CviQI

Specifies that the cutting sequence has to be using.

hidden
type: string
default: ^TAC

Specifies that the cutoff value used for mappability filter.

type: number
default: 0.5

trim 5’ end with the string if not skip_cutadapt

type: string
default: ^TAC

shift size for MACS2

type: integer
default: -75

extsize for MACS2

type: integer
default: 150

cutoff qvalue

type: number
default: 0.01

resolution bin size

type: string
default: 5000_10000

output of restriction_cut_multipleenzyme.py.

type: string
default: None

MAPS regression cutoff value

type: integer
default: 12

MAPS regression fold change cutoff value

type: number
default: 2

MAPS regression -log10(fdr) cutoff value

type: number
default: 2

MAPS regression filter file name

type: string
default: None

MAPS regression type

type: string

remove duplicates for high resolution peaks or not

hidden
type: boolean

Type of snow cluster to use

type: string
default: SOCK

The block number of peak pair

hidden
type: number
default: 1000000000

The minimal number reads count of peak pair

hidden
type: integer
default: 1

create cooler files for MAPS or not

hidden
type: boolean

FDR cutoff value

type: number
default: 0.05

The predefined modle download prefix string

type: string
default: http://3dgenome.fsm.northwestern.edu/peakachu/HiCAR-models/HiCAR-peakachu-pretrained.

Call high resolution peaks or not

type: boolean

cutoff pvalue for fragment (R1)

type: number
default: 0.1

The resolution for compartments calling

type: integer
default: 100000

The resolution for TADs calling

type: integer
default: 10000

The caller for TADs, available choices: ‘cooltools’, ‘hicexplorer’, ‘homer’

type: string

The APA peak path

type: string
default: Anchor 1D peaks

APA tool, available choices: ‘cooltools’, ‘hicexplorer’, and ‘juicebox’

type: string

The APA output figure format. Currently this parameter will not affect the Juicer output format (always png format).

type: string
default: png

Call compartment tool, available choices: ‘cooltools’, ‘hicexplorer’, ‘homer’, and ‘juicebox’

type: string

Call loops tool, available choices: ‘maps’, ‘hicdcplus’, and ‘peakachu’

type: string

Differential analysis tool. Possible options are ‘edger’, ‘diffhic’, ‘hicexplorer’, and ‘setOperation’

type: string

virtual 4c tool, available choices: ‘cooltools’, ‘hicexplorer’, and ‘trackviewer’

type: string

Transcription Factor Enrichment Analysis tool, available choices: ‘atacseqtfea’, and ‘homer’

type: string

juicer_tools jar file url

type: string
default: https://github.com/aidenlab/JuicerTools/releases/download/v3.0.0/juicer_tools.3.0.0.jar

Normalization methods

type: string

parameter for HiCExplorer ChicSignificantinterations

type: integer
default: 2

extension file name for MAPS

hidden
type: string
default: sig3Dinteractions.pe.txt

extension file name for long pairs

hidden
type: string
default: long.bedpe

extension file name for short pairs

hidden
type: string
default: shrt.vip.bed

Options for tracks viewed by igv, ucsc genome browser and virtual 4c plot tools

max events to plot for virtual 4c

type: integer
default: 25

The HiCTools path

type: string
default: https://github.com/aidenlab/HiCTools/releases/download/v3.30.00/hic_tools.3.30.00.jar

skip peak QC or not

hidden
type: boolean

skip plot profile or not

hidden
type: boolean

skip creat IGV files or not

hidden
type: boolean

skip create trackhub files or not

hidden
type: boolean

cutoff value for false discovery rate of enrichment analysis

hidden
type: number

Parameters used to describe centralised config profiles. These should not be edited.

Git commit id for Institutional configs.

hidden
type: string
default: master

Base directory for Institutional configs.

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/configs/master

Institutional config name.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string

Set the top limit for requested resources for any single job.

Maximum number of CPUs that can be requested for any single job.

hidden
type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

hidden
type: string
default: 128.GB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Maximum amount of time that can be requested for any single job.

hidden
type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

Less common options for the pipeline, typically set in a config file.

Display help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

Email address for completion summary, only when pipeline fails.

hidden
type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Send plain-text email instead of HTML.

hidden
type: boolean

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

Do not use coloured log outputs.

hidden
type: boolean

Incoming hook URL for messaging service

hidden
type: string

Custom config file to supply to MultiQC.

hidden
type: string

Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file

hidden
type: string

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

hidden
type: boolean

To skip some processes or workflows.

skip trim 5’end

type: boolean

resample the pairs by pairtools

type: boolean

skip fastqc or not

type: boolean

skip peak annotation or not

type: boolean

skip differential analysis or not

type: boolean

skip multiqc or not

type: boolean

run APA or not

type: boolean

skip call compartment or not

type: boolean

skip call TADs or not

type: boolean

skip call interactions/loops

type: boolean

Do Transcription Factor Enrichment Analysis or not

type: boolean

create track files for virtual 4c or not

type: boolean

skip circos plot

type: boolean