nf-core/createtaxdb
Parallelised and automated construction of metagenomic classifier databases of different tools
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$You will need to create a design file with information about the reference genomes you wish to build into a metagenomic profiling database. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See usage docs.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$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.
stringSpecify name that resulting databases will be prefixed with.
stringNCBI-style four-column accession to taxonomy ID map file
stringAn NCBI four column file tab-separated file with accession, accession.version, taxid and gi number. The first refers to an accession ID in each FASTA entry header. The second refers to the accession ID but with the accession version number appended to the end (e.g. .1). The third refers to the taxonomy ID of the organism the sequence belongs to, as listed in nodes.dmp. The fourth refers to the old-style NCBI gi number of the sequence.
If building with typical NCBI data, the most typical file is the nucl_gb.accession2taxid file from the [NCBI taxonomy FTP server](https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/.
Two column protein sequence accession ID to taxonomy map file.
stringA two column file tab-separated file with accession.version and taxid. The first refers to an accession ID in each FASTA entry header. The second refers to the taxonomy ID of the organism the sequence belongs to, as listed in nodes.dmp.
Two column nucleotide sequence accession ID to taxonomy map file.
stringA two column file tab-separated file with accession.version and taxid. The first refers to an accession ID in each FASTA entry header. The second refers to the taxonomy ID of the organism the sequence belongs to, as listed in nodes.dmp.
Path to NCBI-style taxonomy node dmp file.
stringA tab/pipe/tab separated table file. See nodes.dmp section of NCBI taxdump README for column file structure.
Path to NCBI-style taxonomy names dmp file.
stringA tab/pipe/tab separated table file. See names.dmp section of NCBI taxdump README for column file structure.
Path to MEGAN6/MALT mapping db file
stringA mapping DB file containing taxonomy information for building MALT databases. This file can be downloaded from the MEGAN6 website. Can be zipped (the pipeline will unzip this for you if necessary). Typically the megan-nucl-Feb2022.db.zip is used with MALT.
Save concatenated input FASTAs
booleanSome tools require a single input FASTA of all reference genomes. The pipeline will do this concatenation for you, and by supplying this flag you can save the resulting single fasta for you in the results directory under cat/.
Turn on extending of Kraken2 database to include Bracken files. Requires nucleotide FASTA File input.
booleanBracken2 databases are simply just a Kraken2 database with two additional files.
Note however this requires a Kraken2 database with intermediate files still in it, thus can result in large database directories.
Turn on building of Centrifuge database. Requires nucleotide FASTA file input.
booleanTurn on building of DIAMOND database. Requires amino-acid FASTA file input.
booleanTurn on building of Kaiju database. Requires amino-acid FASTA file input.
booleanTurn on building of MALT database. Requires nucleotide FASTA file input.
booleanSpecify type of input sequence being given to MALT
stringUse to specify whether the reference sequences are DNA or Protein sequences. (For RNA sequences, use the DNA setting) - from MALT manual.
Modifies tool(s) parameter(s)
- malt-build:
--sequenceType
Turn on building of Kraken2 database. Requires nucleotide FASTA file input.
booleanRetain intermediate Kraken2 build files for inspection.
booleanTurn on building of KrakenUniq database. Requires nucleotide FASTA file input.
booleanParameters 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.
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
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.
Validation of parameters in lenient more.
booleanAllows string values that are parseable as numbers or booleans. For further information see JSONSchema docs.
Base URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/