Introduction Usage Parameters Output

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.

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

type: string
pattern: ^\S+\.csv$

You will need to create a design file with information about the BAM files in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See usage docs.

Path to comma-separated file containing the counts for the samples in the experiment. Can also be a file containing just gene identifiers. In this case, count values need to be referenced in the counts_design file.

type: string
pattern: ^\S+\.(csv|txt)$

You will need to create a counts file with the counts for 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 a header row. See usage docs.

Path to comma-separated file containing information about the counts file.

type: string
pattern: ^\S+\.csv$

You will need to create a counts design file with information about the counts file 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 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})$

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 pipeline itself.

Merge samples with the same condition and assay.

type: boolean

If you have multiple samples with the same condition and assay, you can set this parameter to true to merge them into a single sample. This is useful if you have technical replicates and want to combine them into a single sample for analysis.

Minimum number of samples that a peak has to occur in to keep it while merging.

type: integer
default: 1

If you have multiple samples with the same condition and assay and use the --merge_samples parameter, you can set this parameter to the minimum number of samples that a peak has to occur in to keep it while merging.

Size of the window to search for binding sites.

type: integer
default: 50000

Size of the window to search for binding sites. The default value is 50000.

Use decay in STARE

type: boolean
default: true

Use decay in STARE. The default value is true.

Method to aggregate expression values.

type: string
default: mean

Method to aggregate expression values. The default value is mean.

Method to aggregate affinity values.

type: string
default: max

Method to aggregate affinity values. The default value is max.

Number of ChromHMM states.

type: integer
default: 10

Number of ChromHMM states. The default value is 10.

Threshold for ChromHMM enhancer detection.

type: number
default: 0.75

Threshold for ChromHMM enhancer detection. The default value is 0.9.

Comma-separated ChromHMM enhancer marks.

type: string
default: H3K27ac,H3K4me1

ChromHMM enhancer marks. The default value is H3K27ac.

Comma-separated ChromHMM promoter marks.

type: string
default: H3K4me3

ChromHMM promoter marks. The default value is H3K4me3.

TSS window in base pairs

type: integer
default: 2500

ROSE window size around transcription start sites

Stichting window in base pairs

type: integer
default: 12500

ROSE window size for stitching two regions together

Minimum number of total counts to keep a gene in the analysis.

type: integer
default: 50

Minimum number of total counts to keep a gene in the analysis. The default value is 50.

Minimum TPM to keep a gene in the analysis.

type: number
default: 1

Minimum TPM to keep a gene in the analysis. The default value is 1.

Minimum number of total counts to keep a transcription factor in the analysis.

type: integer
default: 50

Minimum number of total counts to keep a transcription factor in the analysis. The default value is 50.

Minimum TPM to keep a transcription factor in the analysis.

type: number
default: 1

Minimum TPM to keep a transcription factor in the analysis. The default value is 1.

Number of outer folds for dynamite.

type: integer
default: 3

Number of outer folds for dynamite. The default value is 3.

Number of inner folds for dynamite.

type: integer
default: 6

Number of inner folds for dynamite. The default value is 6.

Alpha value for dynamite.

type: number
default: 0.1

Alpha value for dynamite. The default value is 0.1.

Randomize the data for dynamite.

type: boolean
default: false

Randomize the data for dynamite. The default value is false.

Minimum regression value for dynamite.

type: number
default: 0.1

Minimum regression value for dynamite. The default value is 0.1.

Alpha value for the Mann-Whitney U test.

type: number
default: 0.05

Alpha value for the Mann-Whitney U test. The default value is 0.05.

Reference genome related files and options required for the workflow.

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

This parameter is mandatory if --genome is not specified.

Path to GTF gene annotation file.

type: string
pattern: ^\S+\.gtf(\.gz)?$

This parameter is mandatory if --genome is not specified.

Path to blacklist regions file.

type: string
pattern: ^\S+\.bed(\.gz)?$

This parameter is mandatory if --genome is not specified.

Path to transcription factor motifs file.

type: string
pattern: ^\S+\.(cisbp|homer|jaspar|meme|transfac|uniprobe)?$

This parameter is mandatory if --genome is not specified. Alternatively, you can use the --taxon_id parameter to fetch the motifs from the JASPAR database.

NCBI Taxonomy ID.

type: integer

This parameter is mandatory if --genome and --motifs are not specified. Use this parameter to fetch the motifs from the JASPAR database.

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.

The base path to the igenomes reference files

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

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

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

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.

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

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.

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/
On this page