nf-core/viralrecon

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

NGS platform used to sequence the samples.

Specifies the type of protocol used for sequencing.

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

Email address for completion summary.

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

Name of viral reference genome.

Path to FASTA genome file.

Full path to GFF annotation file.

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

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

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

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

The primer set to be used for the data analysis.

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

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

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

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

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

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

Sequencing summary file generated after Nanopore run completion.

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

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

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

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

Primer scheme recognised by the artic minion command.

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

Skip pycoQC.

Skip NanoPlot.

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

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

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

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

Skip the bootstrapping module of Freyja

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

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

Specify the number of bootstrap repeats to do.

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

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

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

Skip Pangolin lineage analysis for genome consensus sequence.

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

Skip generation of QUAST aggregated report for consensus sequences.

Skip long table generation for reporting variants.

Skip MultiQC.

Full path to Kraken2 database built from host genome.

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

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

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

Save the trimmed FastQ files in the results directory.

Skip FastQC.

Skip Kraken2 process for removing host classified reads.

Skip the initial read trimming step peformed by fastp.

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

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

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

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.

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

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.

Filtered duplicates reads detected by Picard MarkDuplicates from alignments.

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

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

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

Skip picard MarkDuplicates step.

Skip Picard CollectMultipleMetrics steps.

Skip SnpEff and SnpSift annotation of variants.

Skip creation of consensus base density plots.

Skip genome consensus creation step and any downstream QC.

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

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

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

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

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

Skip Bandage image creation for assembly visualisation.

Skip blastn of assemblies relative to reference genome.

Skip ABACAS process for assembly contiguation.

Skip assembly report generation by PlasmidID.

Skip generation of QUAST aggregated report for assemblies.

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

Minimum contig length to filter from BLAST results.

Minimum percentage of contig aligned to filter from BLAST results.

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.

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

Custom MultiQC yaml file containing HTML including a methods description.