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$

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?s?a(sta)?(\.gz)?$

Do not load the iGenomes reference config.

hidden
type: boolean

The base path to the igenomes reference files

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

Full path to directory containing Bowtie index

type: string

Full path to directory containing Bwa-mem index

type: string

Define the Hi-C processing subworkflow to use to extract the valid pairs from raw data

Hi-C processing method

type: string

Parameters for protocols based on restriction enzyme

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

type: string

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

type: string

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

type: string

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

type: string

Full path to restriction fragment (bed) file.

type: string

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

type: boolean

Parameters for protocols which are not based on restriction enzymes

For Hi-C protocols which are not based on enzyme digestion such as DNAse Hi-C or Micro-C

type: boolean

Minimum distance between loci to consider. Useful for —no-digestion mode to remove spurious ligation products. Only values > 0 are considered

type: integer

Parameters for reads aligments

Split the reads into chunks before running the pipelne

type: boolean

Read number per chunks if split_fastq is used

type: integer
default: 20000000

Keep aligned reads with a minimum quality value

type: integer
default: 10

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

type: string
default: --very-sensitive --end-to-end --reorder

Option for HiC-Pro trimmed reads mapping

type: string
default: --very-sensitive --end-to-end --reorder

Option for Bwa-mem mapping

type: string
default: -5SP -T0

Save all BAM files during two-steps mapping

type: boolean

Options to call significant interactions

Keep duplicated reads

type: boolean

Keep multi-aligned reads

type: boolean

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

type: integer

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

type: integer

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

type: integer

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

type: integer

Update ‘pairtools parse’ options

type: string
default: --walks-policy 5unique

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

type: boolean

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

type: boolean

Options to build Hi-C contact maps

Resolution to build the maps (comma separated)

type: string
default: 1000000
pattern: ^(\d+)(,\d+)*$

Generate raw and normalized contact maps with HiC-Pro

type: boolean

Filter low counts rows before HiC-Pro normalization

type: number
default: 0.02

Filter high counts rows before HiC-Pro normalization

type: integer

Threshold for HiC-Pro ICE convergence

type: number
default: 0.1

Maximum number of iteraction for HiC-Pro ICE normalization

type: integer
default: 100

Update ‘cooler balance’ options

type: string
default: --force

Maximum resolution to build mcool file

type: string

Save raw contact maps

type: boolean

Set up downstream analysis from contact maps

Resolution to build count/distance plot

type: string
default: 250000
pattern: ^(\d+)(,\d+)*$

Define methods for TADs calling

type: string
default: insulation

Define methods for compartments calling

type: string
default: cooltools

Resolution to run TADs callers (comma separated)

type: string
default: 40000
pattern: ^(\d+)(,\d+)*$

Resolution for compartments calling

type: string
default: 250000
pattern: ^(\d+)(,\d+)*$

Skip some steps of the pipeline

Do not build contact maps

type: boolean

Do not run distance/decay plot

type: boolean

Do not run TADs calling

type: boolean

Do not run compartments calling

type: boolean

Do not run cooler balancing normalization

type: boolean

Do not generate mcool file for Higlass visualization

type: boolean

Do not generate MultiQC report

type: boolean

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

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

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

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/

Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.

hidden
type: string