nf-core/viralmetagenome
Detect iSNV and construct whole viral genomes from metagenomic samples
0.1.1). The latest
stable release is
0.1.2
.
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$You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringSample metadata that is included in the multiqc report
string^\S+\.[tc]sv$Email address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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
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.
stringSpecify the maximum number of mismatches between reads for them to still be considered neighbors.
integer1Specify the strategy for umi-deduplication directional vs cluster
stringSpecify the strategy or method for umi-tools deduplication on mapping level
stringDiscard R1 / R2 if required 0, meaning not to discard
integerThe used trimming tool
stringSkip read trimming
booleanUse Fastp's deduplicate option
booleanDefine the accuracy used for hashes while deduplicating with faspt
numberFasta 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 the 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
booleantrueLow-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
Reference 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 conamination
strings3://ngi-igenomes/test-data/viralrecon/kraken2_human.tar.gzKraken2 library(s) required to remove host and contamination
stringhumanOnly used when no host kraken2 database is specified.
Skip the fastqc step after host & contaminants were removed
booleanParameters 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
stringParameters relating to the used assembly methods
Skip de novo assembly of reads
booleanThe specified tools for denovo assembly, multiple options are possible
stringspades,trinity,megahit^(trinity|spades|megahit)(?:,(trinity|spades|megahit)){0,2}$specific SPAdes mode to run
stringFile or directory with amino acid HMMs for Spades HMM-guided mode.
stringPath to yml file containing read information.
stringThe raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) in addition to this YML. File entries in this yml must contain only the file name and no paths.
Regex pattern to identify contigs that have been made by the assemblers
stringParameters relating to the refinement of denovo contigs
Skip the refinement/polishing of contigs through reference based scaffolding and read mapping
booleanSave intermediate polishing files
booleanThere are multiple processes within the polishing subworkflow that might not contain relevant information
Set of fasta sequences used as potential references for the contigs
stringhttps://rvdb.dbi.udel.edu/download/C-RVDBvCurrent.fasta.gzSkip the preclustering of assemblies to facilitate downstream processing of assemblies
booleanKeep the contigs that could not be classified with the taxonomic databases (kaiju_db & kraken2_db)
booleantrueWithin the preclustering step, all contigs will get a taxonomic classification using the provided databases for the metagenomic tools. In some cases, the number of unclassified contigs, can be very large if the database is restrictive. This will result in large clusters in downstream processing that can take up a lot of resources despite not being a priority in some analyses. So set it to True if you want to keep unclassified contigs and set it to False if you don't want to keep them.
Specify the metagenomic classifiers to use for contig taxonomy classification: 'kraken2,kaiju'
stringkraken2,kaiju^(kaiju|kraken2)(,(kaiju|kraken2))?$Taxon conflict resolution mode, must be 1 (Kaiju), 2 (Kraken), lca, or lowest.
stringThe option -c determines the method of resolving conflicts in the taxonomic assignment for a read. Possible values are '1', '2', 'lca', 'lowest': '1' -> the taxon id from Kaiju is used. '2' -> the taxon id from Kraken is used. 'lca' -> the least common ancestor of the two taxon ids from both input files is used. 'lowest' -> the lower rank of the two taxa is used if they are within the same lineage. Otherwise the LCA is used.
Level of taxonomic simplification
stringThe taxonomic classification of the contigs can be simplified to a certain level. This can be done by specifying the taxonomic rank to which the classification should be simplified.
Hard constrain for taxa to exclude from the preclustering, if multiple given make sure to enclose with '"' and separate with a space.
string^[\d +]+$The taxonomic classification of the contigs can be filtered. This can be done by specifying a list of taxa that should be excluded from the results.
Taxon ids to exclude along with all their children from the preclustering, if multiple given make sure to enclose with '"' and separate with a space.
string^[\d +]+$The taxonomic classification of the contigs can be filtered. This can be done by specifying a list of taxa that should be excluded along with all their children from the results.
Taxon ids to exclude along with all their parents from the preclustering, if multiple given make sure to enclose with '"' and separate with a space.
string^[\d +]+$The taxonomic classification of the contigs can be filtered. This can be done by specifying a list of taxa that should be excluded along with all their parents from the results.
Taxon ids to include along with all their children from the preclustering, if multiple given make sure to enclose with '"' and separate with a space.
string^[\d +]+$The taxonomic classification of the contigs can be filtered. This can be done by specifying a list of taxa that should be included along with all their children from the results.
Taxon ids to include along with all their parents from the preclustering, if multiple given make sure to enclose with '"' and separate with a space.
string^[\d +]+$The taxonomic classification of the contigs can be filtered. This can be done by specifying a list of taxa that should be included along with all their parents from the results.
Cluster algorithm used for contigs
string(only with mash) Algorithm to partition the network.
stringMash 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.
booleanIdentity threshold value used in clustering algorithms
number0.6Minimum allowed contig size
integer500Setting this to a low value will result in a large number of questionable contigs and an increase in computation time
Maximum 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
booleanSetting 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.
Define parameters for iterations to update denovo 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
booleanWill always be done when iterative consensus caller is bcftools
consensus 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
booleantrueIf used with umi's, umi tools will be used to group and call consensus of each indiual read group. If not used with umi's use PicardsMarkDuplicates.
Define the variant caller to use: 'ivar' or 'bcftools'
stringconsensus tool used for calling new consensus in final iteration
stringUMI seperator in fastq header.
string:If you have used an alternative method which does not separate the read id and UMI with a “_”, such as bcl2fastq which uses “:”, you can specify the separator with the option --umi_separator=<sep>, replacing <sep> with e.g “:”.
Specify the sketch size, the number of (non-redundant) min-hashes that are kept.
integer4000Larger sketches will better represent the sequence, but at the cost of larger sketch files and longer comparison times.
Specify the kmer size for mash to create their hashes
integer15larger k-mers will provide more specificity, while smaller k-mers will provide more sensitivity. Larger genomes will also require larger k-mers to avoid k-mers that are shared by chance
Define the minimum number of mapped reads in order to continue the variant and consensus calling
integer200calculate summary statistics in final iteration
booleantrueDirectory containing the mutliqc headers for multiple tables like 'clusters_summary_mqc.txt', 'blast_mqc.txt', ...
string${projectDir}/assets/mqc_commentstringApply 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
stringIf not given, the most recent one is downloaded.
Skip the annotation of the consensus constructs
booleanDatabase used for annotation of the cosensus constructs
stringhttps://viralzone.expasy.org/resources/Virosaurus/2020%5F4/virosaurus90%5Fvertebrate-20200330.fas.gzThe metada fields are stored in the fasta comment as key1:"value1"|key2:"value2"|... see docs/databases.md for more information.
Skip 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
booleanSpecify the search algorithm to use for mmseqs. 0: auto 1: amino acid, 2: translated, 3: nucleotide, 4: translated nucleotide alignment
integer4Only search-type 3 supports both forward and reverse search 1 - BLASTP; 2 - TBLASTN; 3 - BLASTN; 4 - TBLASTX
Parameters 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/masterIf 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.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
stringSet the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.h^(\d+\.?\s*(s|m|h|d|day)\s*)+$Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Less common options for the pipeline, typically set in a config file.
Display help text.
booleanDisplay version and exit.
booleanMethod used to save pipeline results to output directory.
stringThe 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.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.
Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
stringIncoming 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.
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
stringCustom MultiQC yaml file containing HTML including a methods description.
stringDelete the output directory if the pipeline fails
booleanCustom yaml file contian g the table column names selection and new names.
string${projectDir}/assets/custom_table_headers.ymlBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBy default, parameters set as hidden in the schema are not shown on the command line when a user runs with --help. Specifying this option will tell the pipeline to show all parameters.
Validation of parameters fails when an unrecognised parameter is found.
booleanBy default, when an unrecognised parameter is found, it returns a warinig.
stringglobal_prefixValidation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Prefix of all output files followed by [date][pipelineversion][runName]
stringUse '--global_prefix' to not have metadata embedded.
Global prefix set if you don't want metadata embedded in the prefix
string