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

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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
???


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