4.22. contigs

4.22.1. Inputs

4.22.1.1. Required inputs

contigs.reads_unmapped_bam
File — Default: None
???

contigs.spades.spades_n_reads
Int — Default: 10000000
Subsample reads threshold prior to assembly. Default set to 10000000

contigs.spades.trim_clip_db
File — Default: None
Trimmomatic clip database.

4.22.1.2. Other inputs

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

contigs.deplete.cpu
Int? — Default: 8
???

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

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.deplete_blastDbs
Array[File] — Default: []
???

contigs.deplete_bmtaggerDbs
Array[File] — Default: []
???

contigs.deplete_bwaDbs
Array[File] — Default: []
???

contigs.rmdup_ubam.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

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

contigs.rmdup_ubam.method
String — Default: "mvicuna"
mvicuna or cdhit

contigs.spades.always_succeed
Boolean — Default: false
In the event that assembly fails for any reason, output an empty contigs file instead of an error code.

contigs.spades.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.33.0"
???

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: None
Minimum length of output contig.

contigs.spades.spades_options
String? — Default: None
Display additional options to pass the SPAdes assembler.

4.22.2. Outputs

contigs.cleaned_reads_unaligned_bam
File?
???

contigs.contigs_fastas
File
???

contigs.deduplicated_reads_unaligned
File
???

contigs.deplete_viral_classify_version
String?
???

contigs.read_counts_dedup
Int
???

contigs.read_counts_depleted
Int?
???

contigs.read_counts_prespades_subsample
Int
???

contigs.read_counts_raw
Int?
???

contigs.spades_viral_assemble_version
String
???

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