Either a tab-seperated sample sheet, a fasta file, or a folder containing zipped FastQ files

required
type: string

Forward primer sequence

required
type: string

Reverse primer sequence

required
type: string

Path to metadata sheet, when missing most downstream analysis are skipped (barplots, PCoA plots, …).

type: string

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

If data is single-ended PacBio reads instead of Illumina

type: boolean

If data is single-ended IonTorrent reads instead of Illumina

type: boolean

If data is single-ended Illumina reads instead of paired-end

type: boolean

If data is long read ITS sequences, that need to be cut to ITS region only for taxonomy assignment

type: boolean

If samples were sequenced in multiple sequencing runs

type: boolean

If analysing ITS amplicons or any other region with large length variability with Illumina paired end reads

type: boolean

Not recommended: When paired end reads are not sufficiently overlapping for merging.

type: boolean

Mode of sample inference: “independent”, “pooled” or “pseudo”

type: string

Comma separated list of metadata column headers for statistics.

type: string

Naming of sequencing files

type: string
default: /*_R{1,2}_001.fastq.gz

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})$

Cutadapt will retain untrimmed reads, choose only if input reads are not expected to contain primer sequences.

type: boolean

Cutadapt will be run twice to ensure removal of potential double primers

type: boolean

DADA2 read truncation value for forward strand, set this to 0 for no truncation

type: integer

DADA2 read truncation value for reverse strand, set this to 0 for no truncation

type: integer

If —trunclenf and —trunclenr are not set, these values will be automatically determined using this median quality score

type: integer
default: 25

Assures that values chosen with —trunc_qmin will retain a fraction of reads.

type: number
default: 0.75

DADA2 read filtering option

type: integer
default: 2

DADA2 read filtering optio

type: string
default: Inf

DADA2 read filtering option

type: integer
default: 50

Name of supported database, and optionally also version number

type: string

If the expected amplified sequences are extracted from the DADA2 reference taxonomy database

type: boolean

Name of supported database, and optionally also version number

type: string

Path to QIIME2 trained classifier file (typically *-classifier.qza)

type: string

Comma separated list of unwanted taxa, to skip taxa filtering use “none”

type: string
default: mitochondria,chloroplast

Abundance filtering

type: integer
default: 1

Prevalence filtering

type: integer
default: 1

Skip FastQC

type: boolean

Skip all steps that are executed by QIIME2, including QIIME2 software download, taxonomy assignment by QIIME2, barplots, relative abundance tables, diversity analysis, differential abundance testing.

type: boolean

Skip taxonomic classification

type: boolean

Skip producing barplot

type: boolean

Skip producing any relative abundance tables

type: boolean

Skip alpha rarefaction

type: boolean

Skip alpha and beta diversity analysis

type: boolean

Skip differential abundance testing

type: boolean

Skip MultiQC reporting

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

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

Run this workflow with Conda. You can also use ‘-profile conda’ instead of providing this parameter.

hidden
type: boolean

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

hidden
type: string

Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.

hidden
type: boolean

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

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+(\.\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*(s|m|h|day)\s*)+$