Folder containing paired-end demultiplexed FastQ files

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

If samples were sequenced in multiple sequencing runs

type: boolean

Path to tab-separated table with sample IDs and paths to sequencing files

type: string

DADA2 read filtering option

type: integer
default: 2

DADA2 read filtering option [PacBio only]

type: integer
default: 2999

DADA2 read filtering option [PacBio only]

type: integer
default: 50

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

Path to taxonomic reference database, currently accepts a qiime compatible file Silva_132_release.zip or a UNITE fasta file

type: string
default: https://www.arb-silva.de/fileadmin/silva_databases/qiime/Silva_132_release.zip

Specify which database to use for taxonomic assignment. Either ‘silva’ or ‘unite’ (default: ‘silva’).

type: string
default: silva

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

type: string

Remove all hash signs from taxonomy strings, resolves a rare ValueError during classification (process classifier)

type: boolean

Dereplication of the database. Must bematching SILVA v132 and its subfolders. Database size is descreasing, but taxonomical assignments as well.

hidden
type: integer
default: 99

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

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

Path to test sequencing read files

hidden
type: string

Comma separated list of metadata column headers for statistics.

type: string

If PacBio data. Use this option together with —manifest

type: boolean

If the sequencing data has PHRED 64 encoded quality scores, otherwise PHRED 33 is assumed

type: boolean

A string that will be used between the prepended run/folder name and the sample name. Only used with “—multipleSequencingRuns”.

type: string
default: -

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})$

Needs to be specified to resolve a timezone error

type: string
default: Europe/Berlin

Keep additional intermediate files, such as trimmed reads or various QIIME2 archives

type: boolean

Skip all steps after importing into QIIME2, used for visually choosing DADA2 parameter --trunclenf and --trunclenr

type: boolean

Path to imported reads (e.g. “demux.qza”)

type: string

Skip all steps after denoising, produce only sequences and abundance tables on ASV level

type: boolean

Skip FastQC

type: boolean

Skip alpha rarefaction

type: boolean

Skip producing barplot

type: boolean

Skip taxonomic classification

type: boolean

Skip producing any relative abundance tables

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

Workflow name.

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

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
hidden
type: string
hidden
type: string
hidden
type: string
default: eu-west-1

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 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

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

hidden
type: string
default: 240.h