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$

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.

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

required
type: string

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

type: string

Save genome reference data to the output directory

type: boolean

Save any technical replicate FASTQ files that were merged to the output directory

type: boolean

Save trimmed FASTQ files to the output directory

type: boolean

Save BAM files aligned to the spike-in genome to the output directory

type: boolean

Save unaligned sequences to the output directory

type: boolean

Save alignment intermediates to the output directory (WARNING: can be very large)

type: boolean

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.

Reference genome related files and options.

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 bowtie2 index

type: string

Path to GTF annotation file

type: string

Path to gene BED file

type: string

Path to genome blacklist

type: string

Name of the iGenome reference for the spike-in genome, defaulting to E. coli K12, for yeast set to R64-1-1, for fruit fly BDGP6

type: string
default: K12-MG1655

Path to spike-in bowtie2 index

type: string

Path to spike-in fasta

type: string

Path to FASTA genome file.

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

This parameter is mandatory if --genome is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with --save_reference to save BWA index for future runs.

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.

Run pipeline up to input checking

type: boolean

Run pipeline up to reference preparation

type: boolean

Run pipeline up to pre-alignment

type: boolean

Run pipeline up to alignment

type: boolean

Run pipeline up to q-filtering

type: boolean

Run pipeline up to peak calling

type: boolean

Skips fastqc reporting

type: boolean

Skips trimming

type: boolean

Skips de-duplication

type: boolean

Skips reporting

type: boolean

Skips preseq reporting

type: boolean

Skips igv session generation

type: boolean

Skips deeptools QC repoting

type: boolean

Skips deeptools heatmap generation

type: boolean

Skips peak QC reporting

type: boolean

Skips multiqc

type: boolean

Instructs Trim Galore to remove bp from the 5' end of read 1 (or single-end reads).

type: integer

Instructs Trim Galore to remove bp from the 5' end of read 2 (paired-end reads only).

type: integer

Instructs Trim Galore to remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.

type: integer

Instructs Trim Galore to remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed.

type: integer

Instructs Trim Galore to apply the --nextseq=X option, to trim based on quality after removing poly-G tails.

type: integer

This enables the option Cutadapt --nextseq-trim=3'CUTOFF option via Trim Galore, which will set a quality cutoff (that is normally given with -q instead), but qualities of G bases are ignored. This trimming is in common for the NextSeq- and NovaSeq-platforms, where basecalls without any signal are called as high-quality G bases.

Select aligner

hidden
type: string
default: bowtie2

Normalisation constant for spike-in read normalisation

hidden
type: integer
default: 10000

Filter reads below a q-score threshold

type: integer

Filter mitochondrial reads

type: boolean

Name of mitochondrial reads in reference genome. Only necessary when using a custom (non-igenomes) reference genome.

type: string

De-duplicate target reads AND control reads (default is control only)

type: boolean

De-duplicate reads based on read 1 5' start position. Relevant for assays using linear amplification with tagmentation (default is false).

type: boolean

Use --end-to-end mode of Bowtie2 during alignment

type: boolean
default: true

Sets the target read normalisation mode. Options are: ["Spikein", "RPKM", "CPM", "BPM", "None" ]

type: string

If normsalisation option is one of "RPKM", "CPM", "BPM" - then the binsize that the reads count is calculated on is used.

type: integer
default: 1

Selects the peak caller for the pipeline. Options are: [seacr, macs2]. More than one peak caller can be chosen and the order specifies which is a primary peak called (the first) that will be used downstream. Any secondary peak callers will be run and outputed to the results folder.

type: string
default: seacr

Specifies whether to use a control to normalise peak calls against (e.g. IgG)

type: boolean
default: true

Specifies whether to extend paired-end fragments between the read mates when calculating coveage tracks

type: boolean
default: true

Specifies whether the background control is scaled prior to being used to normalise peaks.

type: number
default: 0.5

SEACR specifies returns the top n fraction (between 0 and 1) of peaks based on total signal within peaks. This is only used if there are no controls included with the samples and if --use_control is false

type: number
default: 0.05

SEACR normalization.

type: string

SEACR stringency.

type: string

Q-value threshold for MACS2 peak caller.

type: number
default: 0.01

P-value threshold for macs2 peak caller. If set it will overide the qvalue.

type: number

parameter required by MACS2. If using an iGenomes reference these have been provided when --genome is set as GRCh37, GRCh38, GRCm38, WBcel235, BDGP6, R64-1-1, EF2, hg38, hg19 and mm10. Otherwise the gsize will default to GRCh38.

type: number
default: 2700000000

Determines whether MACS2 broad or narrow peak mode is used for the peak caller

type: boolean
default: true

MACS2 broad cutoff parameter

type: number
default: 0.1

Specifies what samples to group together for consensus peaks. Options are [group, all]

type: string

Minimum number of overlapping replicates needed for a consensus peak

type: number
default: 1

Show gene names instead of symbols in IGV browser sessions

type: boolean
default: true

Deeptools multiBamSummary bam bin size

type: integer
default: 500

Deeptools Correlation Plot statistical calculation method

type: string
default: pearson

Deeptools heatmap gene plot before length (bases)

type: integer
default: 3000

Deeptools heatmap gene plot body length (bases)

type: integer
default: 5000

Deeptools heatmap gene plot after length (bases)

type: integer
default: 3000

Deeptools heatmap peak plot before length (bases)

type: integer
default: 3000

Deeptools heatmap peak plot after length (bases)

type: integer
default: 3000

Flag for whether to generate a heatmap for all samples together

type: boolean
default: true

Minimum fragment overlap for FriP score

type: number
default: 0.2

Minimum peak overlap for peak reproducibility plot

type: number
default: 0.2

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

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 this parameter.

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

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
pattern: ^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$

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
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

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'

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

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.

Pull Docker container.

type: boolean

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})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

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

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

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

By default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

By default, when an unrecognised parameter is found, it returns a warinig.

Validation of parameters in lenient more.

hidden
type: boolean

Allows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.