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

Input FastQ files.

required
type: string

Use this to specify the location of your input FastQ files. For example:

--input 'path/to/data/sample_*_{1,2}.fastq'  

Please note the following requirements:

  1. The path must be enclosed in quotes
  2. The path must have at least one * wildcard character
  3. When using the pipeline with paired end data, the path must use {1,2} notation to specify read pairs.

If left unspecified, a default pattern is used: data/*{1,2}.fastq.gz

Input FastQ files for test only

hidden
type: string
default: undefined

Split the reads into chunks before running the pipelne

type: boolean
default: false

Read number per chunks if split_fastq is used

type: integer
default: 20000000

Specifies that the input is single-end reads.

type: boolean

By default, the pipeline expects paired-end data. If you have single-end data, you need to specify --single_end on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for --input. For example:

--single_end --input '*.fastq'  

It is not possible to run a mixture of single-end and paired-end files in one run.

The output directory where the results will be saved.

type: string
default: ./results

Email address for completion summary.

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

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

Options for the reference genome indices used to align reads.

Name of iGenomes reference.

type: string

If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. --genome GRCh38.

See the nf-core website docs for more details.

Path to FASTA genome file.

type: string

If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible.

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

hidden
type: boolean

Do not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.

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

type: string

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

type: string

If not specified, the pipeline will build this file from the reference genome file

Full path to restriction fragment (bed) file.

type: string

This file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the --restriction_site option

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

type: boolean

Use this parameter to save all annotations to your results folder. These can then be used for future pipeline runs, reducing processing times.

Parameters for Hi-C data processing

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

type: boolean

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

type: string
default: 'A^AGCTT'

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

type: string
default: 'AAGCTAGCTT

Remove duplicates

type: boolean
default: true

Remove multi-mapped reads

type: boolean
default: true

Remove singleton

type: boolean
default: true

Keep aligned reads with a minimum quality value

type: integer
default: 10

Option for end-to-end bowtie mapping

type: string
default: '--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder'

Option for trimmed reads mapping

type: string
default: '--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder'

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

type: boolean

Save all BAM files during two-steps mapping

type: boolean

Options to call significant interactions

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

type: integer
default: O

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

type: integer
default: 0

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

type: integer
default: 0

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

type: integer
default: 0

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

type: integer
default: 0

Options to build Hi-C contact maps

Resolution to build the maps (comma separated)

type: string
default: '1000000,500000'

Filter low counts rows before normalization

type: string
default: 0.02

Filter high counts rows before normalization

type: integer
default: 0

Threshold for ICE convergence

type: string
default: 0.1

Maximum number of iteraction for ICE normalization

type: integer
default: 100

Skip some steps of the pipeline

Do not build contact maps

type: boolean

Do not normalize contact maps

type: boolean

Do not generate cooler file

type: boolean

Do not generate MultiQC report

type: boolean

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

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

Workflow name.

hidden
type: string

A custom name for the pipeline run. Unlike the core nextflow -name option with one hyphen this parameter can be reused multiple times, for example if using -resume. Passed through to steps such as MultiQC and used for things like report filenames and titles.

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})$

This works exactly as with --email, except emails are only sent if the workflow is not successful.

Send plain-text email instead of HTML.

hidden
type: boolean

Set to receive plain-text e-mails instead of HTML formatted.

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB

If file generated by pipeline exceeds the threshold, it will not be attached.

Do not use coloured log outputs.

hidden
type: boolean

Set to disable colourful command line output and live life in monochrome.

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

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

Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1

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

hidden
type: string
default: 128.GB

Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'

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

hidden
type: string
default: 240.h

Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'

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

Git commit id for Institutional configs.

hidden
type: string
default: master

Provide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.

## Download and use config file with following git commit id  
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96  

Base directory for Institutional configs.

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

If you're running offline, nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell nextflow where to find them with the custom_config_base option. For example:

## Download and unzip the config files  
cd /path/to/my/configs  
wget https://github.com/nf-core/configs/archive/master.zip  
unzip master.zip  
  
## Run the pipeline  
cd /path/to/my/data  
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/  

Note that the nf-core/tools helper package has a download command to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.

Institutional configs hostname.

hidden
type: string

Institutional config description.

hidden
type: string

Institutional config contact information.

hidden
type: string

Institutional config URL link.

hidden
type: string