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$

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

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

shift size for MACS2

type: integer
default: -75

extsize for MACS2

type: integer
default: 150

cutoff qvalue

type: number
default: 0.01

read peak calling for fragment (R1) reads by MACS2

type: boolean

cutoff pvalue for fragment (R1)

type: number
default: 0.1

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

source code path for merge_map.py

hidden
type: string
default: https://raw.githubusercontent.com/ijuric/MAPS/91c9c360092b25a217d91b9ea07eba5dd2ac72f4/bin/utils/genomic_features_generator/scripts/merge_map.py

feature_frag2bin source path

hidden
type: string
default: https://raw.githubusercontent.com/ijuric/MAPS/91c9c360092b25a217d91b9ea07eba5dd2ac72f4/bin/utils/genomic_features_generator/scripts/feature_frag2bin.py

make_maps_runfile source path

hidden
type: string
default: https://raw.githubusercontent.com/ijuric/MAPS/18c1a337f222130d7c5735d051614e2a253d5319/bin/MAPS/make_maps_runfile.py

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

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

create track files for virtual 4c or not

type: boolean

max events to plot for virtual 4c

type: integer
default: 25

JVM heap parameters for juicer

type: string
default: -Xms512m -Xmx4096m

The juicer_tools path

type: string
default: https://s3.amazonaws.com/hicfiles.tc4ga.com/public/juicer/juicer_tools_1.22.01.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|day)\s*)+$

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

Display help text.

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

Custom config file to supply to MultiQC.

hidden
type: string

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean

Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.

hidden
type: boolean

To skip some processes or workflows.

skip trim 5’end TAC

type: boolean

skip fastqc or not

type: boolean

skip peak annotation or not

type: boolean

skip enrichment or not

type: boolean
default: true

skip differential analysis or not

type: boolean

skip multiqc or not

type: boolean