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$

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)?$

Do not load the iGenomes reference config.

hidden
type: boolean

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

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

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

Incoming hook URL for messaging service

hidden
type: string

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

Base URL or local path to location of pipeline test dataset files

hidden
type: string
default: https://raw.githubusercontent.com/nf-core/test-datasets/

Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.

hidden
type: string
hidden
type: string
hidden
type: string
hidden
type: string

Common options across both long and short read preprocessing QC steps

Specify to skip sequencing quality control of raw sequencing reads

type: boolean

Specify the tool used for quality control of raw sequencing reads

type: string

Save reads from samples that went through the adapter clipping, pair-merging, and length filtering steps for both short and long reads

type: boolean

Save only the final reads from all read processing steps in results directory.

type: boolean

Options for adapter clipping, quality trimming and pair-merging

Turns on short read quality control steps (adapter clipping, read filtering etc.)

type: boolean
default: true

Specify which tool to use for short-read QC

type: string

Skip adapter trimming

type: boolean

Specify adapter 1 nucleotide sequence

type: string

Specify adapter 2 nucleotide sequence

type: string

Specify a list of all possible adapters to trim. Overrides —shortread_qc_adapter1/2. Formats: .txt (AdapterRemoval) or .fasta. (fastp).

type: string

Turn on merging of read pairs for paired-end data

type: boolean

Include unmerged reads from paired-end merging in the downstream analysis

type: boolean

Specify the minimum length of reads to be retained

type: integer
default: 50

Perform deduplication of the input reads (fastp only)

type: boolean

Options for adapter clipping, quality trimming, and length filtering

Turns on long read quality control steps (adapter clipping, length filtering etc.)

type: boolean
default: true

Specify which tool to use for adapter trimming.

type: string

Skip long-read trimming

type: boolean

Specify which tool to use for long reads filtering

type: string
default: nanoq

Skip long-read length and quality filtering

type: boolean

Specify the minimum length of reads to be retained

type: integer
default: 1000

Specify the percent of high-quality bases to be retained

type: integer
default: 90

Filtlong only: specify the number of high-quality bases in the library to be retained

type: integer
default: 500000000

Nanoq only: specify the minimum average read quality filter (Q)

type: integer
default: 7

Options for per-sample run-merging

Turn on run merging

type: boolean
default: true

Save reads from samples that went through the run-merging step

type: boolean
default: true

Options for sub-sampling reads

Turn on sub-sampling of reads with Rasusa

type: boolean
default: true

Desired coverage depth when sub-sampling

type: integer
default: 100

Options for short-read mapping

Specify which tool to use for short-read mapping

type: string

Options for long-read mapping

Specify the output format from minimap2 align

type: boolean
default: true

Specify the bam index file extension

type: string
default: bai

Generate CIGAR

type: boolean

Write CIGAR with >65535 operators at the CG tag.

type: boolean
default: true

Path to Clair3 model

type: string

Sequencing platform

type: string
default: ont

Options for creating FASTA consensus files

Specify the coverage at which low coverage regions are masked with N

type: integer
default: 9

Scale the coverage by a constant factor

type: string
default: 1

Maximum non GATC bases (i.e - and N) to allow in consensus FASTA

type: number
default: 0.5