Path to tab-separated sample sheet

type: string

Path to ASV/OTU fasta file

type: string

Path to folder containing zipped FastQ files

type: string

Forward primer sequence

type: string

Reverse primer sequence

type: string

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

type: string

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})$

If data has binned quality scores such as Illumina NovaSeq

type: boolean

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

type: boolean

If using --input_folder: samples were sequenced in multiple sequencing runs

type: boolean

If using --input_folder: naming of sequencing files

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

Set read count threshold for failed samples.

type: integer
default: 1

Ignore input files with too few reads.

type: boolean

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

type: boolean

Sets the minimum overlap for valid matches of primer sequences with reads for cutadapt (-O).

type: integer
default: 3

Sets the maximum error rate for valid matches of primer sequences with reads for cutadapt (-e).

type: number
default: 0.1

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

type: boolean

Ignore files with too few reads after trimming.

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 option

type: integer
default: 50

DADA2 read filtering option

type: integer

Ignore files with too few reads after quality filtering.

type: boolean

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

type: string

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

type: boolean

Post-cluster ASVs with VSEARCH

type: boolean

Pairwise Identity value used when post-clustering ASVs if --vsearch_cluster option is used (default: 0.97).

type: number
default: 0.97

Enable SSU filtering. Comma separated list of kingdoms (domains) in Barrnap, a combination (or one) of “bac”, “arc”, “mito”, and “euk”. ASVs that have their lowest evalue in that kingdoms are kept.

type: string

Minimal ASV length

type: integer

Maximum ASV length

type: integer

Filter ASVs based on codon usage

type: boolean

Starting position of codon tripletts

type: integer
default: 1

Ending position of codon tripletts

type: integer

Define stop codons

type: string
default: TAA,TAG

Name of supported database, and optionally also version number

type: string

Path to a custom DADA2 reference taxonomy database

type: string

Path to a custom DADA2 reference taxonomy database for species assignment

type: string

Comma separated list of taxonomic levels used in DADA2’s assignTaxonomy function

type: string

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

type: boolean

If multiple exact matches against different species are returned

type: boolean

If reverse-complement of each sequences will be also tested for classification

type: boolean

Newick file with reference phylogenetic tree. Requires also --pplace_aln and --pplace_model.

type: string

File with reference sequences. Requires also --pplace_tree and --pplace_model.

type: string

Phylogenetic model to use in placement, e.g. ‘LG+F’ or ‘GTR+I+F’. Requires also --pplace_tree and --pplace_aln.

type: string

Method used for alignment, “hmmer” or “mafft”

type: string

Tab-separated file with taxonomy assignments of reference sequences.

type: string

A name for the run

hidden
type: string

Name of supported database, and optionally also version number

type: string

Path to files of a custom QIIME2 reference taxonomy database (tarball, or two comma-separated files)

type: string

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

type: string

Name of supported database, and optionally also version number

type: string

Path to a custom Kraken2 reference taxonomy database (.tar.gz|.tgz archive or folder)

type: string

Comma separated list of taxonomic levels used in Kraken2. Will overwrite default values.

type: string

Confidence score threshold for taxonomic classification.

type: number

Name of supported database, and optionally also version number

type: string

If ASVs should be assigned to UNITE species hypotheses (SHs). Only relevant for ITS data.

type: boolean

Part of ITS region to use for taxonomy assignment: “full”, “its1”, or “its2”

type: string

Cutoff for partial ITS sequences. Only full sequences by default.

type: integer

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

Comma separated list of metadata column headers for statistics.

type: string

Comma separated list of metadata column headers for plotting average relative abundance barplots.

type: string

Formula for QIIME2 ADONIS metadata feature importance test for beta diversity distances

type: string

If the functional potential of the bacterial community is predicted.

type: boolean

If data should be exported in SBDI (Swedish biodiversity infrastructure) Excel format.

type: boolean

Minimum rarefaction depth for diversity analysis. Any sample below that threshold will be removed.

type: integer
default: 500

Minimum sample counts to retain a sample for ANCOM analysis. Any sample below that threshold will be removed.

type: integer
default: 1

Minimum taxonomy agglomeration level for taxonomic classifications

type: integer
default: 2

Maximum taxonomy agglomeration level for taxonomic classifications

type: integer
default: 6

Path to Markdown file (Rmd)

type: string
default: ${projectDir}/assets/report_template.Rmd

Path to style file (css)

type: string
default: ${projectDir}/assets/nf-core_style.css

Path to logo file (png)

type: string
default: ${projectDir}/assets/nf-core-ampliseq_logo_light_long.png

String used as report title

type: string
default: Summary of analysis results

Path to Markdown file (md) that replaces the ‘Abstract’ section

type: string

Skip FastQC

type: boolean

Skip primer trimming with cutadapt. This is not recommended! Use only in case primer sequences were removed before and the data does not contain any primer sequences.

type: boolean

Skip quality check with DADA2. Can only be skipped when --trunclenf and --trunclenr are set.

type: boolean

Skip annotating SSU matches.

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 steps that are executed by QIIME2 except for taxonomic classification. Skip steps including barplots, relative abundance tables, diversity analysis, differential abundance testing.

type: boolean

Skip taxonomic classification. Incompatible with --sbdiexport

type: boolean

Skip taxonomic classification with DADA2

type: boolean

Skip species level when using DADA2 for taxonomic classification. This reduces the required memory dramatically under certain conditions. Incompatible with --sbdiexport

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

Skip Markdown summary report

type: boolean

Less common options for the pipeline, typically set in a config file.

Specifies the random seed.

type: integer
default: 100

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

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

Show all params when using --help

hidden
type: boolean

Validation of parameters fails when an unrecognised parameter is found.

hidden
type: boolean

Validation of parameters in lenient more.

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.

type: integer
default: 16

Maximum amount of memory that can be requested for any single job.

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.

type: string
default: 240.h
pattern: ^(\d+\.?\s*(s|m|h|d|day)\s*)+$

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

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

hidden
type: string