4.28. deplete_only¶
Taxonomic depletion of reads matching unwanted taxa (such as human).
4.28.1. Inputs¶
4.28.1.1. Required inputs¶
deplete_only.deplete_taxa.raw_reads_unmapped_bam
File — Default: None
unaligned reads in BAM format
4.28.1.2. Other inputs¶
Show/Hide
deplete_only.deplete_taxa.blastDbs
Array[File]? — Default: None
Optional list of databases to use for blastn-based depletion. Sequences in fasta format will be indexed on the fly, pre-blast-indexed databases may be provided as tarballs.
deplete_only.deplete_taxa.bmtaggerDbs
Array[File]? — Default: None
Optional list of databases to use for bmtagger-based depletion. Sequences in fasta format will be indexed on the fly, pre-bmtagger-indexed databases may be provided as tarballs.
deplete_only.deplete_taxa.bwaDbs
Array[File]? — Default: None
Optional list of databases to use for bwa mem-based depletion. Sequences in fasta format will be indexed on the fly, pre-bwa-indexed databases may be provided as tarballs.
deplete_only.deplete_taxa.clear_tags
Boolean? — Default: false
???
deplete_only.deplete_taxa.cpu
Int? — Default: 8
???
deplete_only.deplete_taxa.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.33.0"
???
deplete_only.deplete_taxa.machine_mem_gb
Int? — Default: None
???
deplete_only.deplete_taxa.query_chunk_size
Int? — Default: None
???
deplete_only.deplete_taxa.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???
4.28.2. Outputs¶
deplete_only.cleaned_bam
File
???
deplete_only.cleaned_fastqc
File
???
deplete_only.cleaned_fastqc_zip
File
???
deplete_only.depletion_read_count_post
Int
???
deplete_only.depletion_read_count_pre
Int
???
deplete_only.viral_classify_version
String
???
Generated using WDL AID (1.0.0)