4.18. classify_krakenuniq

Taxonomic classification of reads using krakenuniq v1.

4.18.1. Inputs

4.18.1.1. Required inputs

classify_krakenuniq.krakenuniq.krakenuniq_db_tar_lz4
File — Default: None
Pre-built Kraken database tarball.

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

classify_krakenuniq.krakenuniq.reads_unmapped_bam
Array[File] — Default: None
Reads to classify. May be unmapped or mapped or both, paired-end or single-end.

4.18.1.2. Other inputs

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

classify_krakenuniq.krakenuniq.machine_mem_gb
Int? — Default: None
???

classify_krakenuniq.metag_summary_report.aggregate_taxlevel_focus
String — Default: "species"
species,genus,family,order,class,phylum,kingdom,superkingdom

classify_krakenuniq.metag_summary_report.aggregate_taxon_heading_space_separated
String — Default: "Viruses"
The taxonomic heading to analyze. More than one can be specified.

classify_krakenuniq.metag_summary_report.aggregate_top_N_hits
Int — Default: 5
only include the top N hits from a given sample in the aggregate report

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

4.18.2. Outputs

classify_krakenuniq.krakenuniq_classified_reads
Array[File]
???

classify_krakenuniq.krakenuniq_krona_by_sample
Array[File]
???

classify_krakenuniq.krakenuniq_krona_merged
File
???

classify_krakenuniq.krakenuniq_summary_reports
Array[File]
???

classify_krakenuniq.metagenomics_summary
File
???

classify_krakenuniq.viral_classify_version
String
???

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Generated using WDL AID (1.0.0)