nohuman_run

Tags: human contamination decontamination scrubbing reads kraken2 nohuman sample-scope

Remove human reads from sequencing data.

Uses nohuman to classify and remove human reads from FASTQ files using a Kraken2 database built from Human Pangenome Reference Consortium (HPRC) genomes. Supports paired-end and single-end Illumina reads.

Database Required

Requires the nohuman Kraken2 database. Use the nohuman/download module or provide a pre-existing database via --nohuman_db.

Inputs

record (
    meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path?	Illumina R1 reads (paired-end forward)
r2	Path?	Illumina R2 reads (paired-end reverse)
se	Path?	Single-end Illumina reads
lr	Path?	Long reads (ONT/PacBio)

db: Path

Name	Type	Description
db	Path	Directory or compressed tarball containing the nohuman Kraken2 database

Outputs

record (
    meta: Record,
    special_meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?,
    lr: Path?,
    scrub_report: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
special_meta	Record	A simplified metadata record for downstream report joining
r1	Path?	Scrubbed paired-end forward reads
r2	Path?	Scrubbed paired-end reverse reads
se	Path?	Scrubbed single-end reads
lr	Path?	Scrubbed long reads
scrub_report	Path	Summary report of reads removed during scrubbing
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Nohuman Run Parameters

Parameter	Type	Default	Description
--nohuman_db	string		Path to the nohuman database directory or tarball
--nohuman_confidence	number	0.0	Kraken2 minimum confidence score for classification (0.0-1.0)
--nohuman_human	boolean	false	Invert output to keep only human reads instead of removing them
--nohuman_save_report	boolean	false	Save the Kraken2 classification report

Used By

Subworkflows

• nohuman - Remove human reads from sequencing data using nohuman.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• Kraken2
  Wood DE, Lu J, Langmead B Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. (2019)

Source

View source on GitHub

Version

NOHUMAN_RUN:
    - bactopia-teton: 1.1.3