4.36. filter_classified_bam_to_taxa¶

Taxonomic filtration of reads utilizing output from a classifier such as kraken1/2/uniq. Can filter out or filter to a specified taxonomic grouping.

4.36.1. Inputs¶

filter_classified_bam_to_taxa.filter_bam_to_taxa.classified_bam
File — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.classified_reads_txt_gz
File — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.ncbi_taxonomy_db_tgz
File — Default: None
???

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

filter_classified_bam_to_taxa.filter_bam_to_taxa.exclude_taxa
Boolean — Default: false
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.machine_mem_gb
Int? — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.minimum_hit_groups
Int? — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.out_filename_suffix
String — Default: "filtered"
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.taxonomic_ids
Array[Int]? — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.taxonomic_names
Array[String]? — Default: None
???

filter_classified_bam_to_taxa.filter_bam_to_taxa.withoutChildren
Boolean — Default: false
???

filter_classified_bam_to_taxa.bam_filtered_to_taxa
File
???

filter_classified_bam_to_taxa.classified_taxonomic_filter_read_count_post
Int
???

filter_classified_bam_to_taxa.classified_taxonomic_filter_read_count_pre
Int
???

filter_classified_bam_to_taxa.viral_classify_version
String
???

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