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

Path to comma-separated file containing information about the samples you would like to analyse.

type: string
pattern: ^\S+\.csv$

NGS platform used to sequence the samples.

type: string

Specifies the type of protocol used for sequencing.

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})$

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

type: string

Options for the reference genome indices used to align reads.

Name of viral reference genome.

type: string

Path to FASTA genome file.

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

Full path to GFF annotation file.

type: string
pattern: ^\S+\.gff(\.gz)?$

Full path to additional annotation file in GTF or GFF format.

type: string
pattern: ^\S+(\.gff|\.gtf)(\.gz)?$

Path to directory or tar.gz archive for pre-built Bowtie2 index.

type: string

If the ‘—protocol amplicon’ parameter is provided then iVar is used to trim primer sequences after read alignment and before variant calling.

type: string
pattern: ^\S+\.bed(\.gz)?$

If the ‘—protocol amplicon’ parameter is provided then Cutadapt is used to trim primer sequences from FastQ files before de novo assembly.

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

The primer set to be used for the data analysis.

type: string

Version of the primer set e.g. ‘—primer_set artic —primer_set_version 3’.

type: number

Suffix used in name field of ‘—primer_bed’ to indicate left primer position.

type: string
default: _LEFT

Suffix used in name field of ‘—primer_bed’ to indicate right primer position.

type: string
default: _RIGHT

If generated by the pipeline save reference genome related files to the results folder.

type: boolean

Options exclusive to running the pipeline on Nanopore data using the ARTIC fieldbioinformatics pipeline.

Path to a folder containing fastq files from the Nanopore run.

type: string

Path to a folder containing fast5 files from the Nanopore run.

type: string

Sequencing summary file generated after Nanopore run completion.

type: string
pattern: ^\S+\.txt$

Minimum number of raw reads required per sample/barcode in order to be considered for the downstream processing steps.

type: integer
default: 100

Minimum number of reads required after the artic guppyplex process per sample/barcode in order to be considered for the downstream processing steps.

type: integer
default: 10

Variant caller used when running artic minion (default: ‘nanopolish’).

type: string

Aligner used when running artic minion (default: ‘minimap2’).

type: string

Primer scheme recognised by the artic minion command.

type: string

Parameter passed to artic minion and required when using the ‘—artic_minion_caller medaka’ workflow.

type: string

Skip pycoQC.

type: boolean

Skip NanoPlot.

type: boolean

Options common to both the Nanopore and Illumina workflows in the pipeline.

Full path to Nextclade dataset required for ‘nextclade run’ command.

type: string

Name of Nextclade dataset to retrieve. A list of available datasets can be obtained using the ‘nextclade dataset list’ command.

type: string

Version tag of the dataset to download. A list of available datasets can be obtained using the ‘nextclade dataset list’ command.

type: string

Skip freyja deep SARS-CoV-2 variant analysis using a depth weighted approach.

type: boolean

Skip the bootstrapping module of Freyja

type: boolean

Specify the name where to store UShER database (default: ‘freyja_db’).

type: string
default: freyja_db

Specify a coverage depth minimum which excludes sites with coverage less than the specified value

type: number

Specify the number of bootstrap repeats to do.

type: integer
default: 100

Lineage defining barcodes, default is most recent from UShER database.

type: string

Metadata of lineages that match barcode, default is most recent from UShER database.

type: string

File size limit when attaching MultiQC reports to summary emails.

hidden
type: string
default: 25.MB

Skip genome-wide and amplicon coverage plot generation from mosdepth output.

type: boolean

Skip Pangolin lineage analysis for genome consensus sequence.

type: boolean

Skip Nextclade clade assignment, mutation calling, and sequence quality checks for genome consensus sequence.

type: boolean

Skip generation of QUAST aggregated report for consensus sequences.

type: boolean

Skip long table generation for reporting variants.

type: boolean

Skip MultiQC.

type: boolean

Options to adjust QC, read trimming and host read filtering with Kraken2 for the Illumina workflow.

Full path to Kraken2 database built from host genome.

type: string
default: s3://ngi-igenomes/test-data/viralrecon/kraken2_human.tar.gz

Name for host genome as recognised by Kraken2 when using the ‘kraken2 build’ command.

type: string
default: human

Remove host reads identified by Kraken2 before running variant calling steps in the pipeline.

type: boolean

Remove host reads identified by Kraken2 before running aseembly steps in the pipeline.

type: boolean
default: true

Save the trimmed FastQ files in the results directory.

type: boolean

Skip FastQC.

type: boolean

Skip Kraken2 process for removing host classified reads.

type: boolean

Skip the initial read trimming step peformed by fastp.

type: boolean

Skip the amplicon trimming step with Cutadapt when using —protocol amplicon.

type: boolean

Various options for the variant calling branch of the Illumina workflow.

Specify which variant calling algorithm you would like to use. Available options are ‘ivar’ (default for ‘—protocol amplicon’) and ‘bcftools’ (default for ‘—protocol metagenomic’).

type: string

Specify which consensus calling algorithm you would like to use. Available options are ‘bcftools’ and ‘ivar’ (default: ‘bcftools’).

type: string

Minimum number of mapped reads below which samples are removed from further processing. Some downstream steps in the pipeline will fail if this threshold is too low.

type: integer
default: 1000

This option unsets the ‘-e’ parameter in ‘ivar trim’ to discard reads without primers.

type: boolean

This option sets the ‘-x’ parameter in ‘ivar trim’ so that reads that occur at the specified offset positions relative to primer positions will also be trimmed.

type: integer

Filtered duplicates reads detected by Picard MarkDuplicates from alignments.

type: boolean

Save unaligned reads in FastQ format from Bowtie 2 to the results directory.

type: boolean

Save mpileup files generated when calling variants with iVar variants or iVar consensus.

type: boolean

Skip iVar primer trimming step. Not recommended for —protocol amplicon.

type: boolean

Skip picard MarkDuplicates step.

type: boolean
default: true

Skip Picard CollectMultipleMetrics steps.

type: boolean

Skip SnpEff and SnpSift annotation of variants.

type: boolean

Skip creation of consensus base density plots.

type: boolean

Skip genome consensus creation step and any downstream QC.

type: boolean

Specify this parameter to skip all of the variant calling and mapping steps in the pipeline.

type: boolean

Various options for the de novo assembly branch of the Illumina workflow.

Specify which assembly algorithms you would like to use. Available options are ‘spades’, ‘unicycler’ and ‘minia’.

type: string
default: spades

Specify the SPAdes mode you would like to run (default: ‘rnaviral’).

type: string

Path to profile HMMs specific for gene/organism to enhance SPAdes assembly.

type: string

Path to directory or tar.gz archive for pre-built BLAST database.

type: string

Skip Bandage image creation for assembly visualisation.

type: boolean

Skip blastn of assemblies relative to reference genome.

type: boolean

Skip ABACAS process for assembly contiguation.

type: boolean

Skip assembly report generation by PlasmidID.

type: boolean
default: true

Skip generation of QUAST aggregated report for assemblies.

type: boolean

Specify this parameter to skip all of the de novo assembly steps in the pipeline.

type: boolean

Minimum contig length to filter from BLAST results.

type: integer
default: 200

Minimum percentage of contig aligned to filter from BLAST results.

type: number
default: 0.7

Set this parameter to false to add an X at the begining or end of the primer’s fasta sequence to specify cutadapt that they are non-internal 5’ or 3’ adapters, respectively.

type: boolean

Set this parameter to true when the primer’s for cutadapt are 3’ adapters. Default value is false, as default primers are 5’ adapters.

type: boolean

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

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

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

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

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

Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.

hidden
type: string

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