4.42. kraken2_build

Build a Kraken2 (or 2X) database.

4.42.1. Inputs

4.42.1.1. Required inputs

kraken2_build.build_kraken2_db.db_basename
String — Default: None
A descriptive string used in output filenames. Outputs will be called kraken2-.tar.zst, krona-.tar.zst, and taxdump-.tar.gz

4.42.1.2. Other inputs

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kraken2_build.build_kraken2_db.custom_libraries
Array[File] — Default: []
A list of 'custom' kraken2 databases to include in this build. Headers must be formatted as described in the kraken2 documentation. These are fastas or tarball collections of such fastas--multiple may be provided here.

kraken2_build.build_kraken2_db.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"
???

kraken2_build.build_kraken2_db.kmerLen
Int? — Default: None
(k) K-mer length in bp/aa (Kraken2 defaults: 35 nt, 15 aa)

kraken2_build.build_kraken2_db.machine_mem_gb
Int? — Default: None
???

kraken2_build.build_kraken2_db.maxDbSize
Int? — Default: None
???

kraken2_build.build_kraken2_db.minimizerLen
Int? — Default: None
(l) Minimizer length in bp/aa (Kraken2 defaults: 31 nt, 12 aa)

kraken2_build.build_kraken2_db.minimizerSpaces
Int? — Default: None
(s) Number of bp/aa in minimizer that are ignored in comparisons (Kraken2 defaults: 7 nt, 0 aa)

kraken2_build.build_kraken2_db.protein
Boolean — Default: false
Build a protein (translated search) database. Default is nucleotide.

kraken2_build.build_kraken2_db.standard_libraries
Array[String] — Default: ["archaea", "bacteria", "plasmid", "viral", "human", "fungi", "protozoa", "UniVec_Core"]
A list of 'standard' kraken2 databases to include in this build. Including any values here will cause fresh downloads of data at the time of build. A list of acceptable names is available at https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#custom-databases

kraken2_build.build_kraken2_db.taxonomy_db_tgz
File? — Default: None
Optional tarball of kraken2 taxonomy database directory. Omitting this input will cause a fresh download from NCBI at the time of build.

kraken2_build.build_kraken2_db.zstd_compression_level
Int? — Default: None
???

4.42.2. Outputs

kraken2_build.kraken2_db
File
???

kraken2_build.krona_db
File
???

kraken2_build.taxdump_tgz
File
???


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