3.12. contigs

3.12.1. Inputs

3.12.1.1. Required inputs

contigs.deplete.raw_reads_unmapped_bam
File — Default: None
unaligned reads in BAM format

contigs.spades.trim_clip_db
File — Default: None
???

3.12.1.2. Other inputs

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contigs.deplete.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.

contigs.deplete.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.

contigs.deplete.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.

contigs.deplete.clear_tags
Boolean? — Default: false
???

contigs.deplete.docker
String? — Default: "quay.io/broadinstitute/viral-classify"
???

contigs.deplete.machine_mem_gb
Int? — Default: None
???

contigs.deplete.query_chunk_size
Int? — Default: None
???

contigs.deplete.tags_to_clear_space_separated
String? — Default: "XT X0 X1 XA AM SM BQ CT XN OC OP"
???

contigs.spades.always_succeed
Boolean? — Default: false
???

contigs.spades.docker
String? — Default: "quay.io/broadinstitute/viral-assemble"
???

contigs.spades.machine_mem_gb
Int? — Default: None
???

contigs.spades.sample_name
String — Default: basename(basename(reads_unmapped_bam,".bam"),".taxfilt")
???

contigs.spades.spades_min_contig_len
Int? — Default: 0
???

contigs.spades.spades_n_reads
Int? — Default: 10000000
???

contigs.spades.trinity_n_reads
Int? — Default: 250000
???

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