4.17. classify_kraken2

Taxonomic classification of sequences via kraken2 (or kraken2x, depending on the database provided).

4.17.1. Inputs

4.17.1.1. Required inputs

classify_kraken2.kraken2.kraken2_db_tgz
File — Default: None
Pre-built Kraken database tarball containing three files: hash.k2d, opts.k2d, and taxo.k2d.

classify_kraken2.kraken2.krona_taxonomy_db_tgz
File — Default: None
Krona taxonomy database containing a single file: taxonomy.tab, or possibly just a compressed taxonomy.tab

classify_kraken2.kraken2.reads_bam
File — Default: None
Reads or contigs to classify. May be unmapped or mapped or both, paired-end or single-end.

4.17.1.2. Other inputs

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classify_kraken2.kraken2.confidence_threshold
Float? — Default: None
Kraken2 confidence score threshold (0.0-1.0). See https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#confidence-scoring

classify_kraken2.kraken2.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"
???

classify_kraken2.kraken2.machine_mem_gb
Int — Default: 72
???

classify_kraken2.kraken2.min_base_qual
Int? — Default: None
Minimum base quality used in classification

4.17.2. Outputs

classify_kraken2.kraken2_reads_report
File
???

classify_kraken2.kraken2_summary_report
File
???

classify_kraken2.krona_report_html
File
???

classify_kraken2.viral_classify_version
String
???

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