nf-core/pathogensurveillance
Surveillance of pathogens using population genomics and sequencing
Define where the pipeline should find input data and save output data.
Path to comma/tab-separated file containing information about samples.
string^\S+\.[ct]sv$This TSV/CSV has one row per samples and contains information such as the location of input files, sample ID, labels, etc. Use this parameter to specify its location. See the usage page for details on formatting this file.
Path to comma-separated file containing information about references.
string^\S+\.[ct]sv$This TSV/CSV has one row per reference and contains information such as the location of input files, reference ID, labels, etc. Use this parameter to specify its location. See the usage page for details on formatting this file.
The output directory where the results will be saved. You have to use absolute paths to storage if running on Cloud infrastructure.
stringThe location to save temporary files for processes. This is only used for some processes that produce large temporary files such as PICARD_SORTSAM.
stringThe location to save downloaded files for later use. This is seperate from the cached data (usually stored in the 'work' directory), so that the cache can be cleared without having to repeat many large downloads.
stringpath_surveil_dataEmail 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.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringThe path to the Bakta database folder. This or --download_bakta_db must be included.
stringDownload the database required for running Bakta. This or --bakta_db must be included. For more information, see: https://github.com/oschwengers/bakta?tab=readme-ov-file#database-download
booleantrueNote that this will download gigabytes of information, so if you are planning to do repeated runs without --resume it would be better to download the database manually according to the bakta documentaion and specify it with --bakta_db.
Which type of the Bakta database to download. Must be 'light' (~2Gb) or 'full' (~40Gb).
stringlightlight|fullParameters that modify the analysis done by the pipeline.
Maximum number of samples to analyze. The first n samples will be used.
integer1000Maximum depth of reads to be used for all analyses. Samples with more reads are subsampled to this depth.
number100When selecting references automatically, only consider references with names that appear to be standard latin bionomials (i.e. no numbers or symbols in the first two words).
booleanWhen selecting references automatically, allow assemblies not in RefSeq.
booleanWhen selecting references automatically, allow assemblies that do not have annotations. The pipeline will attempt to annotate these references as needed.
booleanWhen selecting references automatically, allow assemblies that NCBI considers atypical.
booleanThe maximum number/percentage of references representing unique subspecies to download from RefSeq for each species predicited to be in each sample. Samples with similar initial indentifications will usually use the same references, so the total number of references downloaded for a goup of samples will depend on the taxonomic diversity of the samples.
integer,string5The maximum number/percentage of references representing unique species to download from RefSeq for each genus predicited to be in each sample. Samples with similar initial indentifications will usually use the same references, so the total number of references downloaded for a goup of samples will depend on the taxonomic diversity of the samples.
integer,string20The maximum number/percentage of references representing unique genera to download from RefSeq for each family predicited to be in each sample. Samples with similar initial indentifications will usually use the same references, so the total number of references downloaded for a goup of samples will depend on the taxonomic diversity of the samples.
integer,string20The number of references most similar to each sample based on estimated ANI to include in phyogenetic anlyses.
number2Same as the 'n_ref_closest' option except that it only applies to referneces with what apppear to be standard latin binomaial names (i.e. two words with no numbers or symbols). This is intended to ensure that a refernece with an informative name is present even if it is not the most similar.
number1The number of references representing the entire range of ANI relative to each sample. These are meant to provide context for more similar references. For a group of samples, the fewest total references will be selected that satisify this count for each sample.
number5The minimum number of genes needed to conduct a core gene phylogeny. Samples and references will be removed (as allowed by the min_core_samps and min_core_refs options) until this minimum is met.
number10The maximum number of genes used to conduct a core gene phylogeny.
number500The minimum ANI between a sample and potential reference for that reference to be used for mapping reads from that sample. To force all the samples in a report group to use the same reference, set this value very low.
number0.95The minimum number of bases after quality filtering needed to attempt an genome assembly. Samples with few than this amount of bases will be excluded from further analysis.
number100000The maximum number of variants to use for the SNP tree and minimum spanning nextwork produced by the variant analysis. The first N variants are used when more than N are available.
number100000Parameters 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.
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.
stringControls whether output files are copies or links. When the pipeline runs, files are stored in a temporary cache, typically in the work directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details. By default (mixed), small/important files like reports are copied and everything else is linked.
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.
Custom 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.
stringBoolean whether to validate parameters against the schema at runtime
booleantrueShow all params when using --help
booleanBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pathogensurveillance/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string