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

Input FastQ files.

required
type: string

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})$

Options for the reference genome indices used to align reads.

Name of iGenomes reference.

type: string

Organism for small RNA reference.

type: string

Path to small RNA FASTA file

type: string

Path to genome FASTA file.

type: string

Path to genome FASTA index file

type: string

Path to GTF annotation file

type: string

Path to genome STAR index

type: string

Save STAR index if generated within pipeline.

type: boolean

Directory / URL base for iGenomes references.

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

Do not load the iGenomes reference config.

hidden
type: boolean

Define sequencing adapters and UMI options

Sequencing adapter for trimming

type: string
default: AGATCGGAAGAGC

UMI format to move to FastQ header (optional)

type: string
default: False

Deduplicate using UMIs

type: boolean
default: true

UMI separator in the FastQ read name

type: string
default: :

Define peak callers and peak calling options

Which peakcaller(s) to use

type: string

Path to iCount segment file

type: string

iCount half-window setting

type: integer
default: 3

iCount merge-window setting

type: integer
default: 3

Paraclu minimum cluster count

type: integer
default: 10

Paraclu minimum density increase

type: integer
default: 2

Paraclu maximum cluster length

type: integer
default: 200

PureCLIP binding characteristics of protein

type: integer

PureCLIP merge distance

type: integer
default: 8

PureCLIP chromosomes for HMM training

type: string
default: all

Piranha bin size

type: integer
default: 3

Piranha clustering distance

type: integer
default: 3

Define motif finding parameters

Perform motif finding

type: boolean

Sample n peaks for motif finding

type: integer
default: 1000

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

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

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

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

Show all params when using --help

hidden
type: boolean

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\.]+\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|m|h|d)$

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 configs hostname.

hidden
type: string

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