nf-core/viralmetagenome
Detect iSNV and construct whole viral genomes from metagenomic samples
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.
string^\S+\.csv$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringSample metadata that is included in the multiqc report
string^\S+\.[tc]sv$Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Options related to the trimming, low complexity and host removal steps of the reads
Skip read preprocessing and use input reads for downstream analysis
booleanSkip read quality statistics summary tool ‘fastqc’
booleanSave reads after the final preprocessing step
booleantrueSave reads after every preprocessing step
booleanWith or without UMI detection
booleanWith or without UMI extraction
booleantrueSpecify at what level UMI deduplication should occur.
stringDiscard R1 / R2 if required 0, meaning not to discard
integerThe used trimming tool
stringSkip read trimming
booleanFasta file of adapters
stringSpecify true to save files that failed to pass trimming thresholds ending in *.fail.fastq.gz
booleanSpecify true to save all merged reads to a file ending in *.merged.fastq.gz
booleanInputs with fewer than this reads will be filtered out of the “reads” output channel
integer1Skip filtering of low complexity regions in reads
booleantrueSpecify the decomplexifier to use, bbduk or prinseq
stringReference files containing adapter and/or contaminant sequences for sequence kmer matching (used by bbduk)
stringSkip the removal of host read sequences
booleanKraken2 database used to remove host and contamination
strings3://ngi-igenomes/test-data/viralrecon/kraken2_human.tar.gzKraken2 library(s) required to remove host and contamination
stringhumanSkip the fastqc step after host & contaminants were removed
booleanArguments for FastQC tool
string--quietArguments for Fastp tool
string--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50Arguments for Trimmomatic tool
stringILLUMINACLIP:null:2:30:10Arguments for UMI-tools extract
stringArguments for Humid tool
string-a -m 1Arguments for BBDuk tool
stringentropy=0.3 entropywindow=50 entropymask=fArguments for Prinseq tool for reads
stringArguments for Kraken2 tool for host removal
stringParameters used to determine the metagenomic diversity of the sample
Skip determining the metagenomic diversity of the sample
booleanSpecify the taxonomic read classifiers, choices are ‘kaiju,kraken2’
stringkraken2,kaiju^(kaiju|kraken2|bracken)(?:,(kaiju|kraken2|bracken)){0,2}$Save the used databases
booleanLocation of the Kraken2 database
stringhttps://genome-idx.s3.amazonaws.com/kraken/k2_viral_20230314.tar.gzSave classified and unclassified reads as fastq files
booleanSave summary overview of read classifications in a txt file
booleanSave kraken2’s used minimizers
booleanLocation of bracken database
stringhttps://genome-idx.s3.amazonaws.com/kraken/k2_viral_20230314.tar.gzLocation of Kaiju database
stringhttps://kaiju-idx.s3.eu-central-1.amazonaws.com/2023/kaiju_db_rvdb_2023-05-26.tgzLevel of taxa rank that needs to be determined
stringArguments for Kraken2 tool
string--report-minimizer-dataArguments for Kaiju tool
string-vArguments for Kaiju2Table tool
string-e -l speciesArguments for Kaiju2Krona tool
string-v -uArguments for Krona tool
stringArguments for Bracken tool
stringArguments for Kreport2Krona tool
stringParameters relating to the used assembly methods
Skip de novo assembly of reads
booleanThe specified tools for de novo assembly, multiple options are possible
stringspades,megahit^(trinity|spades|megahit)(?:,(trinity|spades|megahit)){0,2}$Specific SPAdes mode to run
stringFile or directory with amino acid HMMs for Spades HMM-guided mode.
stringPath to yml file containing read information.
stringSkip the filtering of low complexity contigs with prinseq
booleanSkip the contig extension with sspace_basic
booleanSpecify the mean distance between the paired reads
integer350Specify the deviation of the mean distance that is allowed.
number0.75Specify the read orientation.
stringFRArguments for SPAdes tool
string--rnaviralArguments for MEGAHIT tool
stringArguments for Trinity tool
string--max_reads_per_graph 100000Arguments for QUAST tool
string--min-contig 0Arguments for SSPACE Basic tool
string-x 1 -o 15 -r 0.75Arguments for Prinseq tool for contigs
string-out_format 1 -lc_dust .20Parameters relating to the refinement of de novo contigs
Skip the refinement/polishing of contigs through reference based scaffolding and read mapping
booleanSave intermediate polishing files
booleanSet of fasta sequences used as potential references for the contigs
stringhttps://rvdb.dbi.udel.edu/download/C-RVDBvCurrent.fasta.gzSkip the preclustering of assemblies to facilitate downstream processing of assemblies
booleanKeep the contigs that could not be classified with the taxonomic databases (kaiju_db & kraken2_db)
booleantrueSpecify the metagenomic classifiers to use for contig taxonomy classification: ‘kraken2,kaiju’
stringkraken2,kaiju^(kaiju|kraken2)(,(kaiju|kraken2))?$Cluster algorithm used for contigs
string(only with mash) Algorithm to partition the network.
stringSkip creation of the hybrid consensus, instead keep the scaffold with ambiguous bases if the depth of scaffolds is not high enough.
booleanIdentity threshold value used in clustering algorithms
number0.85Minimum cumulated sum of mapped read percentages of each member from a cluster group, set to 0 to disable
integer5Minimum allowed contig size
integer500Maximum allowed contig size
integer10000000Define the maximum percentage of ambiguous bases in a contig
integer50Skip the filtering of contigs that did not cluster together with other contigs
booleanArguments for BLAST makeblastdb tool
string-dbtype nuclArguments for BLASTN tool
string-max_target_seqs 5Arguments for BLAST filter tool
string--escore 0.01 --bitscore 50 --percent-alignment 0.80Arguments for Kraken2 tool for contigs
stringArguments for Kaiju tool for contigs
string-vArguments for precluster extraction
string--keep-unclassified true --merge-strategy lcaArguments for CD-HIT tool
string-c 0.85 -mask rRyYkKsSwWmMbBdDhHvVnNArguments for VSEARCH tool
string--maxseqlength 10000000 --id 0.85 --strand both --iddef 0 --no_progress --qmask noneArguments for MMseqs2 linclust tool
string--min-seq-id 0.85 -c 0.700 --cov-mode 2 --cluster-mode 0Arguments for MMseqs2 cluster tool
string--min-seq-id 0.85 -c 0.700 --cov-mode 2 --cluster-mode 0Arguments for VRhyme tool
string--mems 50Arguments for Mash distance tool
string-s 4000 -k 15Arguments for network clustering
string--score 0.85Arguments for cluster extraction
string--perc_reads_contig 5Arguments for Minimap2 alignment
stringArguments for Minimap2 index
stringArguments for Mash sketch tool
string-iArguments for Mash screen tool
stringArguments for selecting reference
stringDefine 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
booleanNumber of iterations
integer2Mapping tool used during iterations
stringVariant caller used during iterations
stringCall variants during the iterations
booleanConsensus tool used for calling new consensus during iterations
stringbcftoolsCalculate summary statistics during iterations
booleantrueParameters relating to the analysis of variants associated to contigs and scaffolds
Skip the analysis of variants for the external reference or contigs
booleanDefine which mapping tool needs to be used when mapping reads to reference
stringSequence to use as a mapping reference instead of the de novo contigs or scaffolds
stringDeduplicate the reads
booleantrueDefine the variant caller to use: ‘ivar’ or ‘bcftools’
stringConsensus tool used for calling new consensus in final iteration
stringDefine the minimum number of mapped reads in order to continue the variant and consensus calling
integer200Minimum allele frequency threshold for calling consensus
number0.75Calculate summary statistics in final iteration
booleantruestringArguments for BWA-MEM2 index
stringArguments for BWA index
stringArguments for BWA MEM
stringArguments for Bowtie2 build
stringArguments for Bowtie2 alignment
string--local --very-sensitive-local --seed 1Arguments for UMI-tools deduplication
string--umi-separator=\':\' --method cluster --unmapped-reads useArguments for Picard MarkDuplicates
string--ASSUME_SORTED true --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp --REMOVE_DUPLICATES trueArguments for Picard CollectMultipleMetrics
string--ASSUME_SORTED true --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmpArguments for custom mpileup
stringArguments for Mosdepth tool
stringArguments for BCFtools mpileup step 1
string--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/ADRArguments for BCFtools mpileup step 2
string--ploidy 2 --keep-alts --keep-masked-ref --multiallelic-caller --variants-onlyArguments for BCFtools mpileup step 3
string--include \'INFO/DP>=10\Arguments for BCFtools norm
string--do-not-normalize --output-type z --multiallelics -anyArguments for BCFtools stats
stringArguments for Samtools stats command
stringArguments for Samtools idxstats command
stringArguments for Samtools flagstat command
stringArguments for Tabix tool
string-p vcf -fArguments for Bedtools merge
stringArguments for Bedtools maskfasta
stringArguments for BCFtools consensus
stringArguments for iVar variants step 1
string-q 20 -m 10Arguments for iVar variants step 2
string--ignore-overlaps --count-orphans --max-depth 0 --no-BAQ --min-BQ 0Arguments for making BED mask
string-a --ignore-overlaps --count-orphans --max-depth 0 --no-BAQ --min-BQ 0Arguments for iVar consensus step 1
string-t 0 -q 20 -m 10 -n NArguments for iVar consensus step 2
string--count-orphans --max-depth 0 --min-BQ 20 --no-BAQ -aaApply different quality control techniques on the generated consensus genomes
Skip the quality measurements on consensus genomes
booleanSkip the use of checkv for quality check
booleanReference database used by checkv for consensus quality control
stringSkip the annotation of the consensus constructs
booleanDatabase used for annotation of the consensus constructs
stringftp://ftp.expasy.org/databases/viralzone/2020_4/virosaurus90_vertebrate-20200330.fas.gzSkip gene estimation & annotation with prokka
booleanDefine a prokka --protein database for protein annotation
stringSkip the use of QUAST for quality check
booleanSkip the blast search of contigs to the provided reference DB
booleanSkip creating an alignment of each the collapsed clusters and each iterative step
booleantrueSpecify the search algorithm to use for mmseqs. 0: auto 1: amino acid, 2: translated, 3: nucleotide, 4: translated nucleotide alignment
integer4Arguments for CheckV tool
string--remove_tmpArguments for MAFFT iterations
string--auto --adjustdirectionArguments for MAFFT QC
string--auto --adjustdirectionArguments for BLASTN QC
string-max_target_seqs 5Arguments for Prokka tool
string--centre X --compliant --force --kingdom VirusesArguments for MMseqs2 search
string--search-type 4 --rescore-mode 3Arguments for QUAST quality control
stringParameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterBase directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterInstitutional config name.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringLess common options for the pipeline, typically set in a config file.
Display version and exit.
booleanMethod used to save pipeline results to output directory.
stringEmail address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringMultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringCustom config file to supply to MultiQC.
stringCustom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
stringhttps://github.com/Joon-Klaps/viralgenie/blob/dev/docs/images/ViralGenie-nf-core-theme.png?raw=trueCustom MultiQC yaml file containing HTML including a methods description.
stringDelete the output directory if the pipeline fails
booleanCustom yaml file containing the table column names selection and new names.
stringhttps://github.com/Joon-Klaps/viralgenie/raw/refs/heads/dev/assets/custom_table_headers.ymlBoolean whether to validate parameters against the schema at runtime
booleantruePrefix of all output files followed by [date][pipelineversion][runName]
stringGlobal prefix set if you don’t want metadata embedded in the output filenames
stringBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/