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$The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
stringEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$MultiQC report title. Printed as page header, used for filename if not otherwise specified.
stringSpecify name that resulting databases will be prefixed with.
stringNCBI-style four-column accession to taxonomy ID map file
stringTwo column protein sequence accession ID to taxonomy map file.
stringTwo column nucleotide sequence accession ID to taxonomy map file.
stringPath to NCBI-style taxonomy node dmp file.
stringPath to NCBI-style taxonomy names dmp file.
stringPath to NCBI or GTDB genome sizes file
stringPath to MEGAN6/MALT mapping db file
stringSpecify the type of MALT mapdb provided, based on the corresponding MALT flag.
stringSave concatenated input FASTAs
booleanTurn on extending of Kraken2 database to include Bracken files. Requires nucleotide FASTA File input.
booleanSpecify parameters being given to bracken build. Must be wrapped in single and double quotes: —bracken_build_options ”‘—your_param’”
stringTurn 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’”
stringTurn 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’”
stringTurn 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’”
stringTurn 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’”
stringSave 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’”
stringSpecify parameters being given to kmcp index. Must be wrapped in single and double quotes: —kmcp_index_options ”‘—your_param’”
stringTurn 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’”
stringRetain 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’”
stringSave 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 DNAOptions for generating input samplesheets for complementary downstream pipelines.
Generate .tar.gz archived versions of all databases
booleanTurn 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.
stringParameters 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/masterInstitutional 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.
stringHow many files to unzip in parallel in a single job.
integer10000Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Send plain-text email instead of HTML.
booleanFile size limit when attaching MultiQC reports to summary emails.
string25.MB^\d+(\.\d+)?\.?\s*(K|M|G|T)?B$Do not use coloured log outputs.
booleanIncoming hook URL for messaging service
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.
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