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$
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
string
Email address for completion summary.
string
^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
string
Specify name that resulting databases will be prefixed with.
string
NCBI-style four-column accession to taxonomy ID map file
string
Two column protein sequence accession ID to taxonomy map file.
string
Two column nucleotide sequence accession ID to taxonomy map file.
string
Path to NCBI-style taxonomy node dmp file.
string
Path to NCBI-style taxonomy names dmp file.
string
Path to NCBI or GTDB genome sizes file
string
Path to MEGAN6/MALT mapping db file
string
Specify the type of MALT mapdb provided, based on the corresponding MALT flag.
string
Save concatenated input FASTAs
boolean
Turn on extending of Kraken2 database to include Bracken files. Requires nucleotide FASTA File input.
boolean
Specify parameters being given to bracken build. Must be wrapped in single and double quotes: —bracken_build_options ”‘—your_param’”
string
Turn on building of Centrifuge database. Requires nucleotide FASTA file input.
boolean
Specify parameters being given to centrifuge-build. Must be wrapped in single and double quotes: —centrifuge_build_options ”‘—your_param’”
string
Turn on building of DIAMOND database. Requires amino-acid FASTA file input.
boolean
Specify parameters being given to diamond makedb. Must be wrapped in single and double quotes: —diamond_build_options ”‘—your_param’”
string
Turn on building of ganon database. Requires nucleotide FASTA file input.
boolean
Specify parameters being given to ganon buildcustom. Must be wrapped in single and double quotes: —ganon_build_options ”‘—your_param’”
string
Turn on building of Kaiju database. Requires amino-acid FASTA file input.
boolean
Specify parameters being given to kaiju-mkbwt. Must be wrapped in single and double quotes: —kaiju_build_options ”‘—your_param’”
string
Save intermediate files otherwise not required for downstream classification.
boolean
Turn on building of KMCP database. Requires nucleotide FASTA file input.
boolean
Specify parameters being given to kmcp compute. Must be wrapped in single and double quotes: —kmcp_compute_options ”‘—your_param’”
string
Specify parameters being given to kmcp index. Must be wrapped in single and double quotes: —kmcp_index_options ”‘—your_param’”
string
Turn on building of Kraken2 database. Requires nucleotide FASTA file input.
boolean
Specify parameters being given to kraken2 build. Must be wrapped in single and double quotes: —kraken2_build_options ”‘—your_param’”
string
Retain intermediate Kraken2 build files for inspection.
boolean
Turn on building of KrakenUniq database. Requires nucleotide FASTA file input.
boolean
Specify parameters being given to krakenuniq build. Must be wrapped in single and double quotes: —krakenuniq_build_options ”‘—your_param’”
string
Save intermediate files otherwise not required for downstream classification.
boolean
Turn on building of MALT database. Requires nucleotide FASTA file input.
boolean
Specify 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 DNA
Options for generating input samplesheets for complementary downstream pipelines.
Generate .tar.gz
archived versions of all databases
boolean
Turn on generation of samplesheets for downstream pipelines.
boolean
Specify 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.
string
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
string
master
Base directory for Institutional configs.
string
https://raw.githubusercontent.com/nf-core/configs/master
Institutional config name.
string
Institutional config description.
string
Institutional config contact information.
string
Institutional config URL link.
string
Less common options for the pipeline, typically set in a config file.
Display version and exit.
boolean
Method used to save pipeline results to output directory.
string
How many files to unzip in parallel in a single job.
integer
10000
Email 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.
boolean
File size limit when attaching MultiQC reports to summary emails.
string
25.MB
^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$
Do not use coloured log outputs.
boolean
Incoming hook URL for messaging service
string
Custom config file to supply to MultiQC.
string
Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file
string
Custom MultiQC yaml file containing HTML including a methods description.
string
Boolean whether to validate parameters against the schema at runtime
boolean
true
Base URL or local path to location of pipeline test dataset files
string
https://raw.githubusercontent.com/nf-core/test-datasets/
Base URL or local path to location of module test dataset files
string
https://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