Description

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

fasta (file)

One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value

*.{$fasta_ext}

fasta_ext (string)

The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas)

db (directory)

Optional directory pointing to checkM database to prevent re-downloading

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]

versions (file)

File containing software versions

versions.yml

checkm_output (directory)

CheckM output directory

*/

checkm_output (file)

Lineage markfer file

lineage.ms

checkm_tsv (file)

CheckM summary completeness statistics table

*.tsv

Tools

checkm
GPL v3

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.