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scrubber

Tags: metagenomics decontamination human-removal read-filtering sample-scope

Remove contaminant sequences from metagenomic data.

This subworkflow removes human and other contaminant sequences from metagenomic reads using deacon (default), nohuman, or the SRA Human Scrubber. It provides flexible contamination removal with detailed reporting and aggregates results across multiple samples.

Take​

reads: Channel<Record>
FieldDescription
metaGroovy Record containing sample information
r1Illumina R1 reads (paired-end)
r2Illumina R2 reads (paired-end)
seSingle-end Illumina reads
lrLong reads (ONT/PacBio)
use_srascrubber: Boolean
use_nohuman: Boolean
nohuman_db: Path?
download_nohuman: Boolean
nohuman_save_as_tarball: Boolean
deacon_db: Path?
download_deacon: Boolean
NameTypeDescription
use_srascrubberBooleanBoolean flag to use SRA Human Scrubber for decontamination
use_nohumanBooleanBoolean flag to use nohuman for decontamination
nohuman_dbPath?Path to nohuman database directory or tarball (used when use_nohuman is true)
download_nohumanBooleanBoolean flag to download the nohuman database instead of using the provided path
nohuman_save_as_tarballBooleanBoolean flag to save downloaded nohuman database as tarball
deacon_dbPath?Path to deacon minimizer index file (.idx) (used when deacon is selected)
download_deaconBooleanBoolean flag to download the deacon index instead of using the provided path

Emit​

Published​

The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.

sample_outputs​

OutputDescription
special_metaSimplified metadata record for downstream report joining
r1Scrubbed paired-end forward reads
r2Scrubbed paired-end reverse reads
seScrubbed single-end reads
lrScrubbed long reads
scrub_reportContamination removal statistics report

run_outputs​

OutputDescription
csvAggregated contamination reports across all samples

Downstream Inputs​

The following emissions are meant to be used as inputs to downstream subworkflows.

scrubbed​

OutputDescription
r1Scrubbed paired-end forward reads
r2Scrubbed paired-end reverse reads
seScrubbed single-end reads
lrScrubbed long reads

scrubbed_extra​

OutputDescription
r1Scrubbed paired-end forward reads
r2Scrubbed paired-end reverse reads
seScrubbed single-end reads
lrScrubbed long reads
fnaAssembly file (passed through)

special_tsv​

OutputDescription
special_metaSimplified metadata record for downstream report joining
scrub_reportContamination removal statistics report

Subworkflow Composition​

This subworkflow calls the following subworkflows:

  • deacon - Remove host reads from sequencing data using deacon.
  • srahumanscrubber - Remove human contamination from sequencing reads for SRA submission.
  • nohuman - Remove human reads from sequencing data using nohuman.

Module Composition​

This subworkflow calls the following modules:

  • csvtk_concat - Concatenate multiple CSV or TSV files into a single table.

Used By​

This subworkflow is used by the following workflows:

  • cleanyerreads - Quality control and optional host read removal from raw sequencing reads.
  • scrubber - Removal of human and contaminant sequences from metagenomic reads.

Citations​

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

Source​

View source on GitHub