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scrubber

Tags: metagenomics decontamination human-removal read-filtering bactopia-tool

Removal of human and contaminant sequences from metagenomic reads.

This Bactopia Tool removes human and other contaminant sequences from metagenomic reads using deacon (default), nohuman, or SRA Human Scrubber. The tool provides flexible contamination removal with detailed reporting of read classification and filtering statistics. It processes paired-end or single-end reads, producing cleaned FASTQ files with human sequences removed and comprehensive reports documenting the decontamination process.

Usage​

Bactopia CLI:

bactopia --wf scrubber \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/scrubber/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs​

Expected Output Files​

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── scrubber-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.deacon.json
│           ├── <SAMPLE_NAME>.scrub.report.tsv
│           ├── <SAMPLE_NAME>_R1.scrubbed.fastq.gz
│           ├── <SAMPLE_NAME>_R2.scrubbed.fastq.gz
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── scrubber-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── scrubber-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── scrubber.tsv
        └── nf-reports
            ├── scrubber-dag.dot
            ├── scrubber-report.html
            └── scrubber-timeline.html

Per-Sample Results​

FileDescription
*.scrubbed.fastq.gzCleaned reads after human sequence removal
*.scrub.report.tsvReport of read classification and removal statistics

Merged Results​

FileDescription
scrubber.tsvMerged TSV file containing scrubber reports from all samples

Audit Trail​

Below are files that can assist you in understanding which parameters and program versions were used.

Logs​

Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

ExtensionDescription
.beginAn empty file used to designate the process started
.errContains STDERR outputs from the process
.logContains both STDERR and STDOUT outputs from the process
.outContains STDOUT outputs from the process
.runThe script Nextflow uses to stage/unstage files and queue processes based on given profile
.shThe script executed by bash for the process
.traceThe Nextflow trace report for the process
versions.ymlA YAML formatted file with program versions

Nextflow Reports​

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

FilenameDescription
scrubber-dag.dotThe Nextflow DAG visualization
scrubber-report.htmlThe Nextflow Execution Report
scrubber-timeline.htmlThe Nextflow Timeline Report
scrubber-trace.txtThe Nextflow Trace report

Parameters​

Required Parameters​

Define where the pipeline should find input data and save output data.

ParameterTypeDefaultDescription
--bactopiastringThe path to bactopia results to use as inputs

csvtk concat Parameters​

ParameterTypeDefaultDescription
--csvtk_concat_optsstringExtra csvtk concat options in quotes

SRA Human Scrubber Parameters​

ParameterTypeDefaultDescription
--use_srascrubberbooleanfalseUse SRAHumanScrubber for scrubbing human reads

Nohuman Download Parameters​

ParameterTypeDefaultDescription
--nohuman_dbstringPath to the nohuman database or directory to download it to
--nohuman_db_versionstringDatabase version to download (default: latest HPRC release)
--nohuman_save_as_tarballbooleanfalseSave the nohuman database as a tarball
--download_nohumanbooleanfalseDownload the nohuman database to the path given by --nohuman_db

Nohuman Run Parameters​

ParameterTypeDefaultDescription
--nohuman_dbstringPath to the nohuman database directory or tarball
--nohuman_confidencenumber0.0Kraken2 minimum confidence score for classification (0.0-1.0)
--nohuman_humanbooleanfalseInvert output to keep only human reads instead of removing them
--nohuman_save_reportbooleanfalseSave the Kraken2 classification report

Deacon Fetch Parameters​

ParameterTypeDefaultDescription
--deacon_index_namestringpanhuman-1Name of the pre-built deacon index to fetch
--download_deaconbooleanfalseDownload the deacon index to the datasets cache
--use_deaconbooleanfalseUse deacon for host read filtering

Deacon Filter Parameters​

ParameterTypeDefaultDescription
--deacon_abs_thresholdinteger2Minimum absolute number of minimizer hits for a match
--deacon_dbstringPath to a pre-existing deacon index (.idx) for host read filtering
--deacon_depletebooleantrueDiscard matching sequences instead of keeping them
--deacon_optsstringAdditional deacon filter options not covered by other parameters
--deacon_prefix_lengthinteger0Search only the first N nucleotides per sequence (0 for all)
--deacon_rel_thresholdnumber0.01Minimum relative proportion (0.0-1.0) of minimizer hits for a match
Filtering Parameters

Use these parameters to specify which samples to include or exclude.

ParameterTypeDefaultDescription
--includestringA text file containing sample names (one per line) to include from the analysis
--excludestringA text file containing sample names (one per line) to exclude from the analysis
Optional Parameters

These optional parameters can be useful in certain settings.

ParameterTypeDefaultDescription
--outdirstringbactopiaBase directory to write results to
--skip_compressionbooleanfalseOutput files will not be compressed
--datasetsstringThe path to cache datasets to
--keep_all_filesbooleanfalseKeeps all analysis files created
Max Job Request Parameters

Set the top limit for requested resources for any single job.

ParameterTypeDefaultDescription
--max_retryinteger3Maximum times to retry a process before allowing it to fail.
--max_cpusinteger4Maximum number of CPUs that can be requested for any single job.
--max_memorystring128.GBMaximum amount of memory that can be requested for any single job.
--max_timestring240.hMaximum amount of time that can be requested for any single job.
--max_downloadsinteger3Maximum number of samples to download at a time
Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

ParameterTypeDefaultDescription
--nfconfigstringA Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.
--publish_dir_modestringcopyMethod used to save pipeline results to output directory. (choices: symlink, rellink, link, copy, copyNoFollow, move)
--infodirstring${params.outdir}/pipeline_infoDirectory to keep pipeline Nextflow logs and reports.
--forcebooleanfalseNextflow will overwrite existing output files.
--cleanup_workdirbooleanfalseAfter Bactopia is successfully executed, the work directory will be deleted.
Institutional config options

Parameters used to describe centralized config profiles. These should not be edited.

ParameterTypeDefaultDescription
--custom_config_versionstringmasterGit commit id for Institutional configs.
--custom_config_basestringhttps://raw.githubusercontent.com/nf-core/configs/masterBase directory for Institutional configs.
--config_profile_namestringInstitutional config name.
--config_profile_descriptionstringInstitutional config description.
--config_profile_contactstringInstitutional config contact information.
--config_profile_urlstringInstitutional config URL link.
Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

ParameterTypeDefaultDescription
--condadirstringDirectory to Nextflow should use for Conda environments
--registrystringquay.ioRegistry to pull Docker containers from.
--datasets_cachestring<HOME>/.bactopia/datasetsDirectory where downloaded datasets should be stored.
--singularity_cachestringDirectory where remote Singularity images are stored.
--singularity_pull_docker_containerbooleanInstead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
--force_rebuildbooleanfalseForce overwrite of existing pre-built environments.
--queuestringgeneral,high-memoryComma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM)
--cluster_optsstringAdditional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'
--container_optsstringAdditional options to pass to Apptainer, Docker, or Singularity. (e.g. Singularity: '-D pwd'
--disable_scratchbooleanfalseAll intermediate files created on worker nodes of will be transferred to the head node.
Helpful Parameters

Uncommonly used parameters that might be useful.

ParameterTypeDefaultDescription
--monochrome_logsbooleanDo not use coloured log outputs.
--nfdirbooleanPrint directory Nextflow has pulled Bactopia to
--sleep_timeinteger5The amount of time (seconds) Nextflow will wait after setting up datasets before execution.
--validate_paramsbooleantrueBoolean whether to validate parameters against the schema at runtime
--helpbooleanDisplay help text.
--wfstringbactopiaSpecify which workflow or Bactopia Tool to execute
--list_wfsbooleanList the available workflows and Bactopia Tools to use with '--wf'
--show_hidden_paramsbooleanShow all params when using --help
--help_allbooleanAn alias for --help --show_hidden_params
--versionbooleanDisplay version text.

Composition​

This workflow uses the following subworkflows:

  • scrubber - Remove contaminant sequences from metagenomic data.

Citations​

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

Source​

View source on GitHub