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{:bash}

:map

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

fasta{:bash}

:file

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

*.{$fasta_ext}

fasta_ext{:bash}

:string

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

db{:bash}

:directory

Optional directory pointing to checkM database to prevent re-downloading

Output

name:type
description
pattern

checkm_output{:bash}

meta{:bash}

:map

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

${prefix}{:bash}

:directory

CheckM output directory

*/

marker_file{:bash}

meta{:bash}

:map

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

${prefix}/lineage.ms{:bash}

:file

Lineage file

*.ms

checkm_tsv{:bash}

meta{:bash}

:map

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

${prefix}.tsv{:bash}

:file

CheckM summary completeness statistics table

*.tsv

versions_checkm{:bash}

${task.process}{:bash}

:string

The name of the process

checkm{:bash}

:string

The name of the tool

checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

checkm{:bash}

:string

The name of the tool

checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//'{:bash}

:eval

The expression to obtain the version of the tool

Tools

checkm
GPL v3

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

ecogenomics.github.io/CheckM github.com/Ecogenomics/CheckM/wiki https://github.com/Ecogenomics/CheckM 10.1101/gr.186072.114
included in
mag
maintainer
Github user jfy133
get in touch
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