Introduction Usage Parameters Output Results Releases

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

Path to comma-separated file containing information about the samples in the experiment.

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

You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

type: string

Sample metadata that is included in the multiqc report

type: string
pattern: ^\S+\.[tc]sv$

Email address for completion summary.

type: string
pattern: ^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$

Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.

Options related to the trimming, low complexity and host removal steps of the reads

Skip read preprocessing and use input reads for downstream analysis

type: boolean

Skip read quality statistics summary tool 'fastqc'

type: boolean

Save reads after the final preprocessing step

type: boolean
default: true

Save reads after every preprocessing step

type: boolean

With or without UMI detection

type: boolean

With or without UMI extraction

type: boolean
default: true

Specify at what level UMI deduplication should occur.

type: string

Discard R1 / R2 if required 0, meaning not to discard

type: integer

The used trimming tool

type: string

Skip read trimming

type: boolean

Fasta file of adapters

type: string

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

type: boolean

Specify true to save all merged reads to a file ending in *.merged.fastq.gz

type: boolean

Inputs with fewer than this reads will be filtered out of the "reads" output channel

type: integer
default: 1

Skip filtering of low complexity regions in reads

type: boolean
default: true

Low-complexity sequences are defined as having commonly found stretches of nucleotides with limited information content (e.g. the dinucleotide repeat CACACACACA). Such sequences can produce a large number of high-scoring but biologically insignificant results in database searches

Specify the decomplexifier to use, bbduk or prinseq

type: string

Reference files containing adapter and/or contaminant sequences for sequence kmer matching (used by bbduk)

type: string

Skip the removal of host read sequences

type: boolean

Kraken2 database used to remove host and contamination

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

Kraken2 library(s) required to remove host and contamination

type: string
default: human

Only used when no host kraken2 database is specified.

Skip the fastqc step after host & contaminants were removed

type: boolean

Arguments for FastQC tool

type: string
default: --quiet

Arguments for Fastp tool

type: string
default: --cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50

Arguments for Trimmomatic tool

type: string
default: ILLUMINACLIP:null:2:30:10

Arguments for UMI-tools extract

type: string

Arguments for Humid tool

type: string
default: -a -m 1

Arguments for BBDuk tool

type: string
default: entropy=0.3 entropywindow=50 entropymask=f

Arguments for Prinseq tool for reads

type: string

Arguments for Kraken2 tool for host removal

type: string

Parameters used to determine the metagenomic diversity of the sample

Skip determining the metagenomic diversity of the sample

type: boolean

Specify the taxonomic read classifiers, choices are 'kaiju,kraken2'

type: string
default: kraken2,kaiju
pattern: ^(kaiju|kraken2|bracken)(?:,(kaiju|kraken2|bracken)){0,2}$

Save the used databases

type: boolean

Location of the Kraken2 database

type: string
default: https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20230314.tar.gz

Save classified and unclassified reads as fastq files

type: boolean

Save summary overview of read classifications in a txt file

type: boolean

Save kraken2's used minimizers

type: boolean

Location of bracken database

type: string
default: https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20230314.tar.gz

Location of Kaiju database

type: string
default: https://kaiju-idx.s3.eu-central-1.amazonaws.com/2023/kaiju_db_rvdb_2023-05-26.tgz

Level of taxa rank that needs to be determined

type: string

Arguments for Kraken2 tool

type: string
default: --report-minimizer-data

Arguments for Kaiju tool

type: string
default: -v

Arguments for Kaiju2Table tool

type: string
default: -e -l species

Arguments for Kaiju2Krona tool

type: string
default: -v -u

Arguments for Krona tool

type: string

Arguments for Bracken tool

type: string

Arguments for Kreport2Krona tool

type: string

Parameters relating to the used assembly methods

Skip de novo assembly of reads

type: boolean

The specified tools for de novo assembly, multiple options are possible

type: string
default: spades,megahit
pattern: ^(trinity|spades|megahit)(?:,(trinity|spades|megahit)){0,2}$

Specific SPAdes mode to run

type: string

File or directory with amino acid HMMs for Spades HMM-guided mode.

type: string

Path to yml file containing read information.

hidden
type: string

The raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) in addition to this YML. File entries in this yml must contain only the file name and no paths.

Skip the filtering of low complexity contigs with prinseq

type: boolean

Skip the contig extension with sspace_basic

type: boolean

Specify the mean distance between the paired reads

type: integer
default: 350

Specify the deviation of the mean distance that is allowed.

type: number
default: 0.75

For instance, a mean of 200 and a sd of 0.75. This means that any pair having a distance between 150 and 250 is allowed.

Specify the read orientation.

type: string
default: FR

Arguments for SPAdes tool

type: string
default: --rnaviral

Arguments for MEGAHIT tool

type: string

Arguments for Trinity tool

type: string
default: --max_reads_per_graph 100000

Arguments for QUAST tool

type: string
default: --min-contig 0

Arguments for SSPACE Basic tool

type: string
default: -x 1 -o 15 -r 0.75

Arguments for Prinseq tool for contigs

type: string
default: -out_format 1 -lc_dust .20

Parameters relating to the refinement of de novo contigs

Skip the refinement/polishing of contigs through reference based scaffolding and read mapping

type: boolean

Save intermediate polishing files

type: boolean

There are multiple processes within the polishing subworkflow that might not contain relevant information

Set of fasta sequences used as potential references for the contigs

type: string
default: https://rvdb.dbi.udel.edu/download/C-RVDBvCurrent.fasta.gz

Skip the preclustering of assemblies to facilitate downstream processing of assemblies

type: boolean

Keep the contigs that could not be classified with the taxonomic databases (kaiju_db & kraken2_db)

type: boolean
default: true

Within the preclustering step, all contigs will get a taxonomic classification using the provided databases for the metagenomic tools. In some cases, the number of unclassified contigs can be very large if the database is restrictive. This will result in large clusters in downstream processing that can take up a lot of resources despite not being a priority in some analyses. So set it to True if you want to keep unclassified contigs and set it to False if you don't want to keep them.

Specify the metagenomic classifiers to use for contig taxonomy classification: 'kraken2,kaiju'

type: string
default: kraken2,kaiju
pattern: ^(kaiju|kraken2)(,(kaiju|kraken2))?$

Cluster algorithm used for contigs

type: string

(only with mash) Algorithm to partition the network.

type: string

Mash creates a distance matrix that gets translated into a network of connectected nodes where the edges represent the similarity. This network is then split up using the specified method.

  • leiden algorithm: a hierarchical clustering algorithm, that recursively merges communities into single nodes by greedily optimizing the modularity
  • [connected_components] algorithm: a clustering algorithm that defines the largest possible communities where each node within a subset is reachable from every other node in the same subset via any edge .

Skip creation of the hybrid consensus, instead keep the scaffold with ambiguous bases if the depth of scaffolds is not high enough.

type: boolean

Identity threshold value used in clustering algorithms

type: number
default: 0.85

Minimum cumulated sum of mapped read percentages of each member from a cluster group, set to 0 to disable

type: integer
default: 5

Setting this variable will remove clusters that have a low cumulated sum of mapped read percentages. This can be used to remove clusters that have a low coverage and are likely to be false positives.

Minimum allowed contig size

type: integer
default: 500

Setting this to a low value will result in a large number of questionable contigs and an increase in computation time

Maximum allowed contig size

type: integer
default: 10000000

Define the maximum percentage of ambiguous bases in a contig

type: integer
default: 50

Skip the filtering of contigs that did not cluster together with other contigs

type: boolean

Setting this to true will cause the pipeline not to remove contigs that don't have similar contigs. Filtering settings can be further specified with min_contig_size and max_n_100kbp.

Arguments for BLAST makeblastdb tool

type: string
default: -dbtype nucl

Arguments for BLASTN tool

type: string
default: -max_target_seqs 5

Arguments for BLAST filter tool

type: string
default: --escore 0.01 --bitscore 50 --percent-alignment 0.80

Arguments for Kraken2 tool for contigs

type: string

Arguments for Kaiju tool for contigs

type: string
default: -v

Arguments for precluster extraction

type: string
default: --keep-unclassified true --merge-strategy lca

Arguments for CD-HIT tool

type: string
default: -c 0.85 -mask rRyYkKsSwWmMbBdDhHvVnN

Arguments for VSEARCH tool

type: string
default: --maxseqlength 10000000 --id 0.85 --strand both --iddef 0 --no_progress --qmask none

Arguments for MMseqs2 linclust tool

type: string
default: --min-seq-id 0.85 -c 0.700 --cov-mode 2 --cluster-mode 0

Arguments for MMseqs2 cluster tool

type: string
default: --min-seq-id 0.85 -c 0.700 --cov-mode 2 --cluster-mode 0

Arguments for VRhyme tool

type: string
default: --mems 50

Arguments for Mash distance tool

type: string
default: -s 4000 -k 15

Arguments for network clustering

type: string
default: --score 0.85

Arguments for cluster extraction

type: string
default: --perc_reads_contig 5

Arguments for Minimap2 alignment

type: string

Arguments for Minimap2 index

type: string

Arguments for Mash sketch tool

type: string
default: -i

Arguments for Mash screen tool

type: string

Arguments for selecting reference

type: string

Define parameters for iterations to update de novo consensus using reference based improvements

Don't realign reads to consensus sequences and redefine the consensus through (multiple) iterations

type: boolean

Number of iterations

type: integer
default: 2

Mapping tool used during iterations

type: string

Variant caller used during iterations

type: string

Call variants during the iterations

type: boolean

Will always be done when iterative consensus caller is bcftools

Consensus tool used for calling new consensus during iterations

type: string
default: bcftools

Calculate summary statistics during iterations

type: boolean
default: true

Parameters relating to the analysis of variants associated to contigs and scaffolds

Skip the analysis of variants for the external reference or contigs

type: boolean

Define which mapping tool needs to be used when mapping reads to reference

type: string

Sequence to use as a mapping reference instead of the de novo contigs or scaffolds

type: string

Deduplicate the reads

type: boolean
default: true

If used with UMI's, umi tools will be used to group and call consensus of each individual read group. If not used with UMI's use PicardsMarkDuplicates.

Define the variant caller to use: 'ivar' or 'bcftools'

type: string

Consensus tool used for calling new consensus in final iteration

type: string

Define the minimum number of mapped reads in order to continue the variant and consensus calling

type: integer
default: 200

Minimum allele frequency threshold for calling consensus

type: number
default: 0.75

Calculate summary statistics in final iteration

type: boolean
default: true
hidden
type: string

Arguments for BWA-MEM2 index

type: string

Arguments for BWA index

type: string

Arguments for BWA MEM

type: string

Arguments for Bowtie2 build

type: string

Arguments for Bowtie2 alignment

type: string
default: --local --very-sensitive-local --seed 1

Arguments for UMI-tools deduplication

type: string
default: --umi-separator=\':\' --method cluster --unmapped-reads use

Arguments for Picard MarkDuplicates

type: string
default: --ASSUME_SORTED true --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp --REMOVE_DUPLICATES true

Arguments for Picard CollectMultipleMetrics

type: string
default: --ASSUME_SORTED true --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp

Arguments for custom mpileup

type: string

Arguments for Mosdepth tool

type: string

Arguments for BCFtools mpileup step 1

type: string
default: --ignore-overlaps --count-orphans --max-depth 800000 --min-BQ 20 --annotate FORMAT/AD,FORMAT/ADF,FORMAT/ADR,FORMAT/DP,FORMAT/SP,INFO/AD,INFO/ADF,INFO/ADR

Arguments for BCFtools mpileup step 2

type: string
default: --ploidy 2 --keep-alts --keep-masked-ref --multiallelic-caller --variants-only

Arguments for BCFtools mpileup step 3

type: string
default: --include \'INFO/DP>=10\

Arguments for BCFtools norm

type: string
default: --do-not-normalize --output-type z --multiallelics -any

Arguments for BCFtools stats

type: string

Arguments for Samtools stats command

type: string

Arguments for Samtools idxstats command

type: string

Arguments for Samtools flagstat command

type: string

Arguments for Tabix tool

type: string
default: -p vcf -f

Arguments for Bedtools merge

type: string

Arguments for Bedtools maskfasta

type: string

Arguments for BCFtools consensus

type: string

Arguments for iVar variants step 1

type: string
default: -q 20 -m 10

Arguments for iVar variants step 2

type: string
default: --ignore-overlaps --count-orphans --max-depth 0 --no-BAQ --min-BQ 0

Arguments for making BED mask

type: string
default: -a --ignore-overlaps --count-orphans --max-depth 0 --no-BAQ --min-BQ 0

Arguments for iVar consensus step 1

type: string
default: -t 0 -q 20 -m 10 -n N

Arguments for iVar consensus step 2

type: string
default: --count-orphans --max-depth 0 --min-BQ 20 --no-BAQ -aa

Apply different quality control techniques on the generated consensus genomes

Skip the quality measurements on consensus genomes

type: boolean

Skip the use of checkv for quality check

type: boolean

Reference database used by checkv for consensus quality control

type: string

If not given, the most recent one is downloaded.

Skip the annotation of the consensus constructs

type: boolean

Database used for annotation of the consensus constructs

type: string
default: ftp://ftp.expasy.org/databases/viralzone/2020_4/virosaurus90_vertebrate-20200330.fas.gz

The metadata fields are stored in the fasta comment as key1:"value1"|key2:"value2"|... see docs/databases.md for more information.

Skip gene estimation & annotation with prokka

type: boolean

Define a prokka --protein database for protein annotation

type: string

Specify a custom protein database for Prokka annotation

Skip the use of QUAST for quality check

type: boolean

Skip the blast search of contigs to the provided reference DB

type: boolean

Skip creating an alignment of each the collapsed clusters and each iterative step

type: boolean
default: true

Specify the search algorithm to use for mmseqs. 0: auto 1: amino acid, 2: translated, 3: nucleotide, 4: translated nucleotide alignment

type: integer
default: 4

Only search-type 3 supports both forward and reverse search 1 - BLASTP; 2 - TBLASTN; 3 - BLASTN; 4 - TBLASTX

Arguments for CheckV tool

type: string
default: --remove_tmp

Arguments for MAFFT iterations

type: string
default: --auto --adjustdirection

Arguments for MAFFT QC

type: string
default: --auto --adjustdirection

Arguments for BLASTN QC

type: string
default: -max_target_seqs 5

Arguments for Prokka tool

type: string
default: --centre X --compliant --force --kingdom Viruses

Arguments for MMseqs2 search

type: string
default: --search-type 4 --rescore-mode 3

Arguments for QUAST quality control

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

If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.

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 version and exit.

hidden
type: boolean

Method used to save pipeline results to output directory.

hidden
type: string

The Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.

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})$

An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.

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

Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.

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

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
default: https://github.com/Joon-Klaps/viralgenie/blob/dev/docs/images/ViralGenie-nf-core-theme.png?raw=true

Custom MultiQC yaml file containing HTML including a methods description.

type: string

Delete the output directory if the pipeline fails

hidden
type: boolean

Custom yaml file containing the table column names selection and new names.

hidden
type: string
default: https://github.com/Joon-Klaps/viralgenie/raw/refs/heads/dev/assets/custom_table_headers.yml

Boolean whether to validate parameters against the schema at runtime

hidden
type: boolean
default: true

Prefix of all output files followed by [date][pipelineversion][runName]

type: string

Use '--global_prefix' to not have metadata embedded.

Global prefix set if you don't want metadata embedded in the output filenames

type: string

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

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