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

Path to comma-separated file containing information sample names and paths to corresponding FASTA files.

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

These parameters influence which workflow (ARG, AMP and/or BGC) to activate.

Activate antimicrobial peptide screening tools.

type: boolean

Activate antimicrobial resistance gene screening tools.

type: boolean

Activate biosynthetic gene cluster screening tools.

type: boolean

These options influence the generation of annotation files required for downstream steps in ARG, AMP, and BGC workflows.

Specify which annotation tool to use for some downstream tools.

type: string

Specify whether to save gene annotations in the results directory.

type: boolean

These parameters influence the annotation algorithm of Bacteria used by BAKTA.

Specify a path to BAKTA database.

type: string
default: None

Specify the minimum contig size.

type: integer
default: 1

Specify the genetic code translation table.

type: integer
default: 11

Specify the type of bacteria to be annotated to detect signaling peptides.

type: string

Specify that all contigs are complete replicons.

type: boolean

Changes the original contig headers.

type: boolean

Clean the result annotations to standardise them to Genbank/ENA conventions.

type: boolean

Skip tRNA detection & annotation.

type: boolean

Skip tmRNA detection & annotation.

type: boolean

Skip rRNA detection & annotation.

type: boolean

Skip ncRNA detection & annotation.

type: boolean

Skip ncRNA region detection & annotation.

type: boolean

Skip CRISPR array detection & annotation.

type: boolean

Skip CDS detection & annotation.

type: boolean

Skip pseudogene detection & annotation.

type: boolean

Skip sORF detection & annotation.

type: boolean

Skip gap detection & annotation.

type: boolean

Skip oriC/oriT detection & annotation.

type: boolean

These parameters influence the annotation algorithm used by Prokka.

Use the default genome-length optimised mode (rather than the metagenome mode).

type: boolean

Suppress the default clean-up of the gene annotations.

type: boolean

Specify the kingdom that the input represents.

type: string

Specify the translation table used to annotate the sequences.

type: integer
default: 11

Minimum contig size required for annotation (bp).

type: integer
default: 1

Minimum e-value cut-off.

type: number
default: 0.000001

Set the assigned minimum coverage.

type: integer
default: 80

Allow transfer RNA (trRNA) to overlap coding sequences (CDS).

type: boolean

Use RNAmmer for rRNA prediction.

type: boolean

Sequencing centre ID.

type: string

Force contig name to Genbank/ENA/DDJB naming rules.

type: boolean

Assign the locus tag for the contig header.

type: string
default: Prokka

Add the gene features for each CDS hit.

type: boolean

These parameters influence the annotation algorithm used by PRODIGAL.

Specify whether to use Prodigal’s single-genome mode for long sequences.

type: boolean

Does not allow partial genes on contig edges.

type: boolean

Specifies the translation table used for gene annotation.

type: integer
default: 11

Forces PRODIGAL to scan for motifs.

type: boolean

Generic options for database downloading

Specify whether to save pipeline-downloaded databases in your results directory.

type: boolean

Antimicrobial Peptide detection using a deep learning model.

Skip AMPlify during AMP-screening.

type: boolean

Antimicrobial Peptide detection using machine learning

Skip AMPir during AMP-screening.

type: boolean

Specify which machine learning classification model to use.

type: string

Specify minimum protein length for prediction calculation.

type: integer
default: 10

Antimicrobial Peptide detection based on predefined HMM models

Skip HMMsearch during AMP-screening.

type: boolean

Specify path to the AMP hmm model file(s) to search against. Must have quotes if wildcard used.

type: string
default: None

Saves a multiple alignment of all significant hits to a file.

type: boolean

Save a simple tabular file summarising the per-target output.

type: boolean

Save a simple tabular file summarising the per-domain output.

type: boolean

Antimicrobial Peptide detection mining from metagenomes

Skip Macrel during AMP-screening.

type: boolean

AntiMicrobial Peptides parsing and functional classification tool

Path to AMPcombi reference database directory.

type: string
default: None

Specify probability cutoff to filter AMPs

type: number
default: 0.4

Antimicrobial resistance gene detection based on NCBI’s curated Reference Gene Database and curated collection of Hidden Markov Models

Skip AMRFinderPlus during the ARG-screening.

type: boolean

Specify the path to a local version of the ARMfinderPlus database.

type: string
default: None

Minimum percent identity to reference sequence.

type: number
default: -1

Minimum coverage of the reference protein.

type: number
default: 0.5

Specify which NCBI genetic code to use for translated BLAST.

type: integer
default: 11

Add the plus genes to the report.

type: boolean

Add identified column to AMRFinderPlus output.

type: boolean

Antimicrobial resistance gene detection using a deep learning model

Skip DeepARG during the ARG-screening.

type: boolean

Specify the path to the DeepARG database.

type: string
default: None

Specify the numeric version number of a user supplied DeepaRG database.

type: integer
default: 2

Specify which model to use (short or long sequences).

type: string

Specify minimum probability cutoff under which hits are discarded.

type: number
default: 0.8

Specify E-value cutoff under which hits are discarded.

type: number
default: 1e-10

Specify percent identity cutoff for sequence alignment under which hits are discarded.

type: integer
default: 50

Specify alignment read overlap.

type: number
default: 0.8

Specify minimum number of alignments per entry for DIAMOND step of DeepARG.

type: integer
default: 1000

Antimicrobial resistance gene detection using a deep learning model

Skip fARGene during the ARG-screening.

type: boolean

Specify comma-separated list of which pre-defined HMM models to screen against

type: string
default: class_a,class_b_1_2,class_b_3,class_c,class_d_1,class_d_2,qnr,tet_efflux,tet_rpg,tet_enzyme

Specify to save intermediate temporary files to results directory.

type: boolean

The threshold score for a sequence to be classified as a (almost) complete gene.

type: number

The minimum length of a predicted ORF retrieved from annotating the nucleotide sequences.

type: integer
default: 90

Defines which ORF finding algorithm to use.

type: boolean

The translation table/format to use for sequence annotation.

type: string
default: pearson

Antimicrobial resistance gene detection, based on alignment to the CARD database

Skip RGI during the ARG-screening.

type: boolean

Specify to save intermediate temporary files the results directory.

type: boolean

Specify the alignment tool to be used.

type: string

Include all of loose, strict and perfect hits (i.e. >=95% identity) found by RGI.

type: boolean
default: true

Suppresses the default behaviour of RGI with --arg_rgi_includeloose.

type: boolean
default: true

Include screening of low quality contigs for partial genes.

type: boolean

Specify a more specific data-type of input (e.g. plasmid, chromosome)

type: string

Antimicrobial resistance gene detection, based on alignment to CBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.

Skip ABRicate during the ARG-screening.

type: boolean

Specify which of the provided public databases to use by ABRicate.

type: string

Minimum percent identity of alignment required for a hit to be considered.

type: integer
default: 80

Minimum percent coverage of alignment required for a hit to be considered.

type: integer
default: 80

Biosynthetic gene cluster detection

Skip antiSMASH during the BGC screening

type: boolean

Path to user-defined local antiSMASH database.

type: string
default: None

Path to user-defined local antiSMASH directory. Only required when running with docker/singularity.

type: string
default: None

Minimum longest-contig length a sample must have to be screened with antiSMASH.

type: integer
default: 1000

Minimum length a contig must have to be screened with antiSMASH.

type: integer
default: 1000

Turn on clusterblast comparison against database of antiSMASH-predicted clusters.

type: boolean

Turn on clusterblast comparison against known gene clusters from the MIBiG database.

type: boolean

Turn on clusterblast comparison against known subclusters responsible for synthesising precursors.

type: boolean

Turn on ClusterCompare comparison against known gene clusters from the MIBiG database.

type: boolean

Generate phylogenetic trees of secondary metabolite group orthologs.

type: boolean

Defines which level of strictness to use for HMM-based cluster detection

type: string

Specify which taxonomic classification of input sequence to use

type: string

A deep learning genome-mining strategy for biosynthetic gene cluster prediction

Skip deepBGC during the BGC screening.

type: boolean

Path to local deepBGC database folder.

type: string
default: None

Average protein-wise DeepBGC score threshold for extracting BGC regions from Pfam sequences.

type: number
default: 0.5

Run DeepBGC’s internal Prodigal step in single mode to restrict detecting genes to long contigs

type: boolean

Merge detected BGCs within given number of proteins.

type: integer

Merge detected BGCs within given number of nucleotides.

type: integer

Minimum BGC nucleotide length.

type: integer
default: 1

Minimum number of proteins in a BGC.

type: integer
default: 1

Minimum number of protein domains in a BGC.

type: integer
default: 1

Minimum number of known biosynthetic (as defined by antiSMASH) protein domains in a BGC.

type: integer

DeepBGC classification score threshold for assigning classes to BGCs.

type: number
default: 0.5

Biosynthetic gene cluster detection

Skip GECCO during the BGC screening.

type: boolean

Enable unknown region masking to prevent genes from stretching across unknown nucleotides.

type: boolean

The minimum number of coding sequences a valid cluster must contain.

type: integer
default: 3

The p-value cutoff for protein domains to be included.

type: number
default: 1e-9

The probability threshold for cluster detection.

type: number
default: 0.8

The minimum number of annotated genes that must separate a cluster from the edge.

type: integer

Biosynthetic Gene Cluster detection based on predefined HMM models

Skip HMMsearch during BGC-screening.

type: boolean

Specify path to the BGC hmm model file(s) to search against. Must have quotes if wildcard used.

type: string
default: None

Saves a multiple alignment of all significant hits to a file.

type: boolean

Save a simple tabular file summarising the per-target output.

type: boolean

Save a simple tabular file summarising the per-domain output.

type: boolean

Influences parameters required for the reporting workflow.

Specifies summary output format

type: string

Reference genome related files and options required for the workflow.

Name of iGenomes reference.

hidden
type: string

Path to FASTA genome file.

hidden
type: string
pattern: ^\S+\.fn?a(sta)?(\.gz)?$

Directory / URL base for iGenomes references.

hidden
type: string
default: s3://ngi-igenomes/igenomes

Do not load the iGenomes reference config.

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 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*)+$

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

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

Directory to keep pipeline Nextflow logs and reports.

hidden
type: string
default: ${params.outdir}/pipeline_info

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Show all params when using --help

hidden
type: boolean