checkm2_download
Tags: checkm2 download database diamond machine-learning sample-scope
Download the pre-trained CheckM2 database.
Fetches the required Diamond database used by CheckM2 for genome quality prediction. This database contains the machine learning model training data.
Internet Required
This process requires an active internet connection to fetch the database.
Outputs
record (
db: Path,
json: Path,
logs: Set<Path?>
)
| Field | Type | Description |
|---|---|---|
db | Path | The CheckM2 Diamond database file (*.dmnd) |
json | Path | Metadata file describing the database contents |
logs | Set<Path?> | Optional program specific log files |
Parameters
CheckM2 Database Download Parameters
| Parameter | Type | Default | Description |
|---|---|---|---|
--checkm2_db | string | Path to a folder containing CheckM2 database (or where it should be downloaded to). | |
--download_checkm2 | boolean | false | Download the CheckM2 database to the path given by --checkm2_db |
Used By
Subworkflows
- checkm2 - Assess metagenome bin completeness using CheckM2.
Workflows
- checkm2 - Machine learning-based assessment of microbial genome assembly quality.
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) -
CheckM2
Chklovksi A Rapid assessment of genome bin quality using machine learning (GitHub)
Source
Version
CHECKM2_DOWNLOAD:
- aria2: 1.36.0