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

Path to tab-separated sample sheet

required
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})$

Parameters for QC and trim short-reads

This can be used to pass arguments to Fastp

type: string

save trimmed files

type: boolean

save files that failed to pass trimming thresholds ending in *.fail.fastq.gz

type: boolean

Skip FastQC

type: boolean

Skip FastP

type: boolean

Path to Kraken2 database.

type: string

Path to the Kmerfinder bacteria database (ie: ‘/path_to/kmerfinder/bacteria/ or ‘/path_to/kmerfinder/bacteria.tar.gz’). Only taxonomic group ‘bacteria’ is allowed. See database installation (guidelines)[https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/] for details. The latest version can be downloaded from the KmerFinder Database FTP site or directly during pipeline execution with. Example:

--kmerfinder_db 'ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/bacteria.tar.gz' (Note: Downloading the KmerFinder database (~30GB) via FTP can be time-consuming. It’s recommended to pre-download the database and provide the *.tar.gz file using this parameter instead of URL site.). An older version is available on (Zenodo)[https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz].

type: string

Reference FASTA file.

type: string

Reference GFF file.

type: string

Master file (*.txt) containing a summary of assemblies available in GeneBank or RefSeq. See: https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt

type: string

Parameters for the assembly

The assembler to use for assembly. Use the appropriate assembler according to the chosen assembly_type. Refer to the README.md for further clarification.

type: string

Which type of assembly to perform.

type: string

Extra arguments for Unicycler

type: string

Allowed technologies for long read assembly.

type: string

This can be used to supply extra options to the Canu assembler. Will be ignored when other assemblers are used.

type: string

Extra arguments for Dragonflye

type: string

Which assembly polishing method to use.

type: string

Parameters for the annotation

The annotation method to annotate the final assembly.

type: string

Extra arguments for prokka annotation tool.

type: string

Path to Bakta database

type: string

Download Bakta database

type: boolean

This can be used to supply extra options to the Bakta download module

type: string

Specifies a configuration file for the DFAST annotation method.

type: string
default: assets/test_config_dfast.py

Skip running Kraken2 classifier on reads.

type: boolean

Skip contamination analysis with Kmerfinder

type: boolean

Skip annotating the assembly with Prokka /DFAST.

type: boolean

Skip running PycoQC on long read input.

type: boolean

Skip polishing the long-read assembly with fast5 input. Will not affect short/hybrid assemblies.

type: boolean

Skip MultiQC

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 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 help text.

hidden
type: boolean

Display version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

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

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

A comma separated string of inputs the schema validation should ignore

hidden
type: string
default: modules,igenomes_base

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

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