4.29. 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.

4.29.1. Inputs

4.29.1.1. Required 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
???

4.29.1.2. Other inputs

Show/Hide

filter_classified_bam_to_taxa.filter_bam_to_taxa.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.10.0"
???

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
???

---

Generated using WDL AID (0.1.1)