inputs.md

Pipeline Inputs

This page documents all input parameters for the pipeline.

Input/output options

--input {#input}

Type: string | Optional | Format: file-path

same as sample_sheet

--sample_sheet {#sample-sheet}

Type: string | Optional

sample sheet with sample, fastq_1, and fastq_2 columns

--reads {#reads}

Type: string | Optional

Directory with paired-end fastq files

--single_reads {#single-reads}

Type: string | Optional

Directory with single-end illumina fastq files

--nanopore {#nanopore}

Type: string | Optional

Directory with nanopore fastq files

--fastas {#fastas}

Type: string | Optional

input channel for fastas

--multifastas {#multifastas}

Type: string | Optional

input channel for multifasta files

--sra_accessions {#sra-accessions}

Type: string | Optional

list encased in [] brackets of fastq accessions to download from SRA/ENA (Illumina reads only)

Default: []

--genome_accessions {#genome-accessions}

Type: string | Optional

list encased in [] brackets of genome accessions to download with datasets

Default: []

--species {#species}

Type: string | Optional

specifies species-specific sub-workflows

Default: sarscov2

Allowed values:

• other
• mpx
• sarscov2

--vadr_reference {#vadr-reference}

Type: string | Optional

Specifies reference for vadr in container

Default: sarscov2

--freyja_pathogen {#freyja-pathogen}

Type: string | Optional

Specifies freyja pathogen

--freyja_update {#freyja-update}

Type: boolean | Optional

Whether to update freyja db

Default: True

--nextclade_dataset {#nextclade-dataset}

Type: string | Optional

Specifies nextclade dataset

Default: sars-cov-2

--iqtree_outgroup {#iqtree-outgroup}

Type: string | Optional

outgroup for multiple sequence alignment

Default: MN908947

--minimum_depth {#minimum-depth}

Type: integer | Optional

minimum depth for calling a variant

Default: 100

--mpileup_depth {#mpileup-depth}

Type: integer | Optional

number of reads put into memory by samtools/bcftools

Default: 8000

--kraken2_db {#kraken2-db}

Type: string | Optional

directory to kraken2 database

--outdir {#outdir}

Type: string | Required | Format: directory-path

The output directory where the results will be saved. Absolute paths are required on cloud infrastructure.

Default: cecret

Reference files

--reference_genome {#reference-genome}

Type: string | Optional

THE Reference genome

--amplicon_bed {#amplicon-bed}

Type: string | Optional

Bedfile for amplicons

--gff {#gff}

Type: string | Optional

File used in ivar variants. Must correspond with reference genome.

--primer_bed {#primer-bed}

Type: string | Optional

File with bedfile of primers used in the analysis

--primer_set {#primer-set}

Type: string | Optional

Specifies a primer set included in repo

Default: ncov_V5.3.2

Allowed values:

• midnight_idt_V1
• midnight_ont_V1
• midnight_ont_V2
• midnight_ont_V3
• ncov_V3
• ncov_V4
• ncov_V4.1
• ncov_V5.3.2
• mpx_primalseq
• mpx_idt

Workflow Components

--cleaner {#cleaner}

Type: string | Optional

Specifies what tool to use to remove low quality reads

Default: seqyclean

Allowed values:

• seqyclean
• fastp

--aligner {#aligner}

Type: string | Optional

Specifies which aligner is going to be used.

Default: bwa

Allowed values:

• bwa
• minimap2

--trimmer {#trimmer}

Type: string | Optional

Specifies which tool to use to trim primers from primerbedfile

Default: ivar

Allowed values:

• samtools
• ivar
• none

--msa {#msa}

Type: string | Optional

Specifies what tool to use for multiple sequence alignment. Current options are only mafft.

Default: mafft

--download_nextclade_dataset {#download-nextclade-dataset}

Type: boolean | Optional

Uses included nextclade dataset for SARS-CoV-2 during runtime when false.

Default: True

--predownloaded_nextclade_dataset {#predownloaded-nextclade-dataset}

Type: string | Optional

Path to predownloaded nextclade dataset

--filter {#filter}

Type: boolean | Optional

Specifies if reference-mapped fastq files should be extracted

--markdup {#markdup}

Type: boolean | Optional

Specifies if duplicate reads should be removed

--relatedness {#relatedness}

Type: boolean | Optional

Turns on multiple sequence alignment subworkflow when true

Toggles

--aci {#aci}

Type: boolean | Optional

Specifies if process should be used

--artic {#artic}

Type: boolean | Optional

Specifies if process should be used

--artic_filter {#artic-filter}

Type: boolean | Optional

Specifies if process should be used

--bbnorm {#bbnorm}

Type: boolean | Optional

Specifies if process should be used

--bcftools_variants {#bcftools-variants}

Type: boolean | Optional

Specifies if process should be used

Default: True

--fastqc {#fastqc}

Type: boolean | Optional

Specifies if process should be used

Default: True

--freyja {#freyja}

Type: boolean | Optional

Specifies if process should be used

Default: True

--freyja_aggregate {#freyja-aggregate}

Type: boolean | Optional

Specifies if process should be used

Default: True

--heatcluster {#heatcluster}

Type: boolean | Optional

Specifies if process should be used

Default: True

--igv_reports {#igv-reports}

Type: boolean | Optional

Specifies if process should be used

--iqtree {#iqtree}

Type: boolean | Optional

Specifies if process should be used

Default: True

--ivar_variants {#ivar-variants}

Type: boolean | Optional

Specifies if process should be used

--kraken2 {#kraken2}

Type: boolean | Optional

Specifies if process should be used

Default: True

--multiqc {#multiqc}

Type: boolean | Optional

Specifies if process should be used

Default: True

--nextclade {#nextclade}

Type: boolean | Optional

Specifies if process should be used

Default: True

--pango_aliasor {#pango-aliasor}

Type: boolean | Optional

Specifies if process should be used

Default: True

--pangolin {#pangolin}

Type: boolean | Optional

Specifies if process should be used

Default: True

--phytreeviz {#phytreeviz}

Type: boolean | Optional

Specifies if process should be used

Default: True

--samtools_qc {#samtools-qc}

Type: boolean | Optional

Specifies if process should be used

Default: True

--samtools_ampliconstats {#samtools-ampliconstats}

Type: boolean | Optional

Specifies if process should be used

Default: True

--samtools_plot_ampliconstats {#samtools-plot-ampliconstats}

Type: boolean | Optional

Specifies if process should be used

Default: True

--snpdists {#snpdists}

Type: boolean | Optional

Specifies if process should be used

Default: True

--vadr {#vadr}

Type: boolean | Optional

Specifies if process should be used

Default: True

Process Adjustments

--aci_options {#aci-options}

Type: string | Optional

Options for process

--artic_read_filtering_options {#artic-read-filtering-options}

Type: string | Optional

Options for process

Default: --min-length 400 --max-length 700

--artic_options {#artic-options}

Type: string | Optional

Options for process

Default: --normalise 200 --model r1041_e82_400bps_sup_v500 --model-dir /opt/conda/envs/artic/bin/models/

--bbnorm_options {#bbnorm-options}

Type: string | Optional

Options for process

Default: target=200 min=5

--bcftools_variants_options {#bcftools-variants-options}

Type: string | Optional

Options for process

--fastp_options {#fastp-options}

Type: string | Optional

Options for process

--fastqc_options {#fastqc-options}

Type: string | Optional

Options for process

--filter_options {#filter-options}

Type: string | Optional

Options for process

--heatcluster_options {#heatcluster-options}

Type: string | Optional

Options for process

Default: -t png

--igv_reports_options {#igv-reports-options}

Type: string | Optional

Options for process

Default: --flanking 1000

--iqtree_options {#iqtree-options}

Type: string | Optional

Options for process

Default: -ninit 2 -n 2 -me 0.05 -m GTR

--ivar_consensus_options {#ivar-consensus-options}

Type: string | Optional

Options for process

Default: -q 20 -t 0.6 -n N

--ivar_trim_options {#ivar-trim-options}

Type: string | Optional

Options for process

--ivar_variants_options {#ivar-variants-options}

Type: string | Optional

Options for process

Default: -q 20 -t 0.6

--mafft_options {#mafft-options}

Type: string | Optional

Options for process

Default: --maxambiguous 0.5

--minimap2_options {#minimap2-options}

Type: string | Optional

Options for process

Default: -K 20M

--multiqc_options {#multiqc-options}

Type: string | Optional

Options for process

--phytreeviz_options {#phytreeviz-options}

Type: string | Optional

Options for process

--pangolin_options {#pangolin-options}

Type: string | Optional

Options for process

--samtools_coverage_options {#samtools-coverage-options}

Type: string | Optional

Options for process

--samtools_ampliconclip_options {#samtools-ampliconclip-options}

Type: string | Optional

Options for process

--samtools_flagstat_options {#samtools-flagstat-options}

Type: string | Optional

Options for process

--samtools_stats_options {#samtools-stats-options}

Type: string | Optional

Options for process

--samtools_ampliconstats_options {#samtools-ampliconstats-options}

Type: string | Optional

Options for process

Default: --max-amplicon-length 3000 --max-amplicons 3000

--samtools_plot_ampliconstats_options {#samtools-plot-ampliconstats-options}

Type: string | Optional

Options for process

Default: -size 1200,900 -size2 1200,900 -size3 1200,900

--samtools_depth_options {#samtools-depth-options}

Type: string | Optional

Options for process

--samtools_markdup_options {#samtools-markdup-options}

Type: string | Optional

Options for process

--samtools_fixmate_options {#samtools-fixmate-options}

Type: string | Optional

Options for process

--seqyclean_options {#seqyclean-options}

Type: string | Optional

Options for process

Default: -minlen 25 -qual

--seqyclean_contaminant_file {#seqyclean-contaminant-file}

Type: string | Optional

Options for process

Default: /Adapters_plus_PhiX_174.fasta

--snpdists_options {#snpdists-options}

Type: string | Optional

Options for process

Default: -c

--nextclade_options {#nextclade-options}

Type: string | Optional

Options for process

--vadr_mdir {#vadr-mdir}

Type: string | Optional

Options for process

Default: /opt/vadr/vadr-models

--freyja_demix_options {#freyja-demix-options}

Type: string | Optional

Options for process

--freyja_update_options {#freyja-update-options}

Type: string | Optional

Options for process

--freyja_variants_options {#freyja-variants-options}

Type: string | Optional

Options for process

--pango_aliasor_options {#pango-aliasor-options}

Type: string | Optional

Options for process

--freyja_aggregate_options {#freyja-aggregate-options}

Type: string | Optional

Options for process

--freyja_plot_options {#freyja-plot-options}

Type: string | Optional

Options for process

--freyja_plot_filetype {#freyja-plot-filetype}

Type: string | Optional

Options for process

Default: png

--kraken2_options {#kraken2-options}

Type: string | Optional

Options for process

--vadr_options {#vadr-options}

Type: string | Optional

Options for process

--vadr_trim_options {#vadr-trim-options}

Type: string | Optional

Options for process

Institutional config options

--custom_config_version {#custom-config-version}

Type: string | Optional

Git commit id for Institutional configs.

Default: master

--custom_config_base {#custom-config-base}

Type: string | Optional

Base directory for Institutional configs.

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.

Default: https://raw.githubusercontent.com/nf-core/configs/master

--config_profile_name {#config-profile-name}

Type: string | Optional

Institutional config name.

--config_profile_description {#config-profile-description}

Type: string | Optional

Institutional config description.

--config_profile_contact {#config-profile-contact}

Type: string | Optional

Institutional config contact information.

--config_profile_url {#config-profile-url}

Type: string | Optional

Institutional config URL link.

Generic options

--help {#help}

Type: boolean | Optional

Display help text.

--version {#version}

Type: boolean | Optional

Display version and exit.

--email {#email}

Type: string | Optional

Email address for completion summary.

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.

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

--publish_dir_mode {#publish-dir-mode}

Type: string | Optional

Method used to save pipeline results to output directory.

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.

Default: copy

Allowed values:

• symlink
• rellink
• link
• copy
• copyNoFollow
• move

--email_on_fail {#email-on-fail}

Type: string | Optional

Email address for completion summary, only when pipeline fails.

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

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

--plaintext_email {#plaintext-email}

Type: boolean | Optional

Send plain-text email instead of HTML.

--monochrome_logs {#monochrome-logs}

Type: boolean | Optional

Do not use coloured log outputs.

--hook_url {#hook-url}

Type: string | Optional

Incoming hook URL for messaging service

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

--pipelines_testdata_base_path {#pipelines-testdata-base-path}

Type: string | Optional

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

Default: https://raw.githubusercontent.com/nf-core/test-datasets/

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This pipeline was built with Nextflow. Documentation generated by nf-docs v0.2.0 on 2026-03-12 23:00:43 UTC.