4.17. classify_single

Runs raw reads through taxonomic classification (Kraken2), human read depletion (based on Kraken2), de novo assembly (SPAdes), and FASTQC/multiQC of reads.

4.17.1. Inputs

4.17.1.1. Required inputs

classify_single.kraken2_db_tgz
File — Default: None
Pre-built Kraken database tarball containing three files: hash.k2d, opts.k2d, and taxo.k2d.

classify_single.krona_taxonomy_db_kraken2_tgz
File — Default: None
Krona taxonomy database containing a single file: taxonomy.tab, or possibly just a compressed taxonomy.tab

classify_single.ncbi_taxdump_tgz
File — Default: None
An NCBI taxdump.tar.gz file that contains, at the minimum, a nodes.dmp and names.dmp file.

classify_single.reads_bam
File — Default: None
Reads to classify. May be unmapped or mapped or both, paired-end or single-end.

classify_single.spikein_db
File — Default: None
ERCC spike-in sequences

classify_single.trim_clip_db
File — Default: None
Adapter sequences to remove via trimmomatic prior to SPAdes assembly

4.17.1.2. Other inputs

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classify_single.deplete.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

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

classify_single.deplete.minimum_hit_groups
Int? — Default: None
???

classify_single.deplete.taxonomic_ids
Array[Int]? — Default: None
???

classify_single.deplete.withoutChildren
Boolean — Default: false
???

classify_single.fastqc_cleaned.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

classify_single.fastqc_raw.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

classify_single.filter_acellular.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

classify_single.filter_acellular.machine_mem_gb
Int? — Default: None
???

classify_single.filter_acellular.minimum_hit_groups
Int? — Default: None
???

classify_single.filter_acellular.taxonomic_ids
Array[Int]? — Default: None
???

classify_single.filter_acellular.withoutChildren
Boolean — Default: false
???

classify_single.kraken2.confidence_threshold
Float? — Default: None
Kraken2 confidence score threshold (0.0-1.0). See https://ccb.jhu.edu/software/kraken2/index.shtml?t=manual#confidence-scoring

classify_single.kraken2.docker
String — Default: "quay.io/broadinstitute/viral-classify:2.1.16.0"
???

classify_single.kraken2.machine_mem_gb
Int? — Default: None
???

classify_single.kraken2.min_base_qual
Int? — Default: None
Minimum base quality used in classification

classify_single.rmdup_ubam.docker
String? — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

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

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

classify_single.spades.docker
String — Default: "quay.io/broadinstitute/viral-assemble:2.1.16.1"
???

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

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

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

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

classify_single.spikein.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.19"
???

classify_single.spikein.machine_mem_gb
Int? — Default: None
???

classify_single.spikein.topNHits
Int — Default: 3
???

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