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.
For more information see the nf-core/createtaxdb FAQ.
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.
If building with typical NCBI data, the most typical file is the prot.accession2taxid.gz file from the NCBI taxonomy FTP server.
For more information see the nf-core/createtaxdb FAQ.
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 used at the beginning of each FASTA entry header. The second refers to the taxonomy ID of the organism the sequence belongs to, as listed in nodes.dmp. Required for Centrifuge, and optional for Kraken2.
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.
For more information see the nf-core/createtaxdb FAQ.
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.
For more information see the nf-core/createtaxdb FAQ.
Path to NCBI or GTDB genome sizes file
stringA tab/pipe/tab separated table file. For NCBI versions see the species_genome_size section of NCBI genome assembly reports README for column file structure.
If not supplied, will be automatically downloaded for you.
For more information see the nf-core/createtaxdb FAQ.
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.
For more information see the nf-core/createtaxdb FAQ.
Specify the type of MALT mapdb provided, based on the corresponding MALT flag.
stringWhile MALT now theoretically supports only a single type of MEGAN mapping file (*.db), in some cases this does not appear to work.
You can however still currently use technically 'deprecated' MEGAN mapping files that end in .abin.
For nf-core/createtaxdb, when specifying the MALT mapping file you therefore also need to specify which format this file is, based on the corresponding (short) MALT flags for malt-build. For example for the new type of mapping file, you can give just mdb. For a nucleotide accession to taxonomy file you give a2t. For a accession to SEED category mapping file, you specify a2seed.
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.
Specify parameters being given to bracken build. Must be wrapped in single and double quotes: --bracken_build_options "'--your_param'"
stringParameters must be wrapped in both single and then double quotes outside these, to ensure the parameters are interpreted as a string for internal use rather than interpreted by the terminal as a pipeline-level parameter.
Turn on building of Centrifuge database. Requires nucleotide FASTA file input.
booleanSpecify parameters being given to centrifuge-build. Must be wrapped in single and double quotes: --centrifuge_build_options "'--your_param'"
stringParameters must be wrapped in both single and then double quotes outside these, to ensure the parameters are interpreted as a string for internal use rather than interpreted by the terminal as a pipeline-level parameter.
Turn on building of DIAMOND database. Requires amino-acid FASTA file input.
booleanSpecify parameters being given to diamond makedb. Must be wrapped in single and double quotes: --diamond_build_options "'--your_param'"
stringParameters must be wrapped in both single and then double quotes outside these, to ensure the parameters are interpreted as a string for internal use rather than interpreted by the terminal as a pipeline-level parameter.
Turn on building of ganon database. Requires nucleotide FASTA file input.
booleanSpecify parameters being given to ganon buildcustom. Must be wrapped in single and double quotes: --ganon_build_options "'--your_param'"
stringSee ganon documentation.
Parameters must be wrapped in both single and then double quotes outside these, to ensure the parameters are interpreted as a string for internal use rather than interpreted by the terminal as a pipeline-level parameter.
Turn on building of Kaiju database. Requires amino-acid FASTA file input.
booleanSpecify parameters being given to kaiju-mkbwt. Must be wrapped in single and double quotes: --kaiju_build_options "'--your_param'"
stringSee Kaiju documentation.
Parameters must be wrapped in both single and then double quotes outside these, to ensure the parameters are interpreted as a string for internal use rather than interpreted by the terminal as a pipeline-level parameter.
Save intermediate files otherwise not required for downstream classification.
booleanTurn on building of KMCP database. Requires nucleotide FASTA file input.
booleanSpecify parameters being given to kmcp compute. Must be wrapped in single and double quotes: --kmcp_compute_options "'--your_param'"
stringSee KMCP documentation.
Parameters must be wrapped in both single and then double quotes outside these, to ensure the parameters are interpreted as a string for internal use rather than interpreted by the terminal as a pipeline-level parameter.
Specify parameters being given to kmcp index. Must be wrapped in single and double quotes: --kmcp_index_options "'--your_param'"
stringSee KMCP documentation.
Parameters must be wrapped in both single and then double quotes outside these, to ensure the parameters are interpreted as a string for internal use rather than interpreted by the terminal as a pipeline-level parameter.
Turn on building of Kraken2 database. Requires nucleotide FASTA file input.
booleanSpecify parameters being given to kraken2 build. Must be wrapped in single and double quotes: --kraken2_build_options "'--your_param'"
stringParameters must be wrapped in both single and then double quotes outside these, to ensure the parameters are interpreted as a string for internal use rather than interpreted by the terminal as a pipeline-level parameter.
Retain intermediate Kraken2 build files for inspection.
booleanTurn on building of KrakenUniq database. Requires nucleotide FASTA file input.
booleanSpecify parameters being given to krakenuniq build. Must be wrapped in single and double quotes: --krakenuniq_build_options "'--your_param'"
stringParameters must be wrapped in both single and then double quotes outside these, to ensure the parameters are interpreted as a string for internal use rather than interpreted by the terminal as a pipeline-level parameter.
Save intermediate files otherwise not required for downstream classification.
booleanTurn on building of MALT database. Requires nucleotide FASTA file input.
booleanSpecify parameters given to malt-build. Must include --sequenceType DNA or Protein and be wrapped in double and single quotes: --malt_build_options "'--sequenceType DNA --your_param'"
string--sequenceType DNAAt least the type of reference sequences should be specified. (For RNA sequences, use the DNA setting) - from MALT manual.
Parameters must be wrapped in both single and then double quotes outside these, to ensure the parameters are interpreted as a string for internal use rather than interpreted by the terminal as a pipeline-level parameter.
Options for generating input samplesheets for complementary downstream pipelines.
Generate .tar.gz archived versions of all databases
booleanMany of the tools create databases that consist of a directory with multiple files.
This option can be useful when you will be downloading taxonomic profiling tools that require remote downloading of files for staging (assuming the tool or pipeline supports decompression of .tar.gz files).
A common use case is running taxonomic profilers in the cloud, and where staging tools do not support downloading of directories. Another is if you have to long-term archive your database for reproducibility purposes.
By giving this flag, .tar.gz files of all the databases will be created in the output directory.
Turn on generation of samplesheets for downstream pipelines.
booleanSpecify a comma separated string in quotes to specify which pipeline to generate a samplesheet for.
string^(taxprofiler)(?:,(taxprofiler)){0,1}Specify which type of database to list paths of in the generated pipeline samplesheet.
stringIt is recommend to select tar if you plan to run the downstream pipeline in the cloud, or similar environments where you cannot easily download directories.
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.
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.
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.
How many files to unzip in parallel in a single job.
integer10000To reduce the load on scheduling systems, nf-core/createtaxdb batches all compressed input FASTA files into this number, and will decompress them in parallel within a single scheduling job (rather than one job per decompression).
This is because decompression jobs are often very short and require few resources.
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
booleantrueBase URL or local path to location of pipeline test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/Base URL or local path to location of module test dataset files
stringhttps://raw.githubusercontent.com/nf-core/test-datasets/modules/data/Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.
string