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 ]

analysis_dir{:bash}

:file

Directory containing output of checkm/analyze or checkm/lineage_wf etc.

*

marker_file{:bash}

:file

Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf

*.ms

coverage_file{:bash}

:file

File containing coverage of each sequence (generated by checkm coverage)

exclude_marker_file{:bash}

:file

File specifying markers to exclude from marker sets

db{:bash}

:directory

CheckM database directory

Output

name:type
description
pattern

output{:bash}

meta{:bash}

:map

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

${prefix}.txt{:bash}

:file

Default completeness statistics in various formats, as specified with —out_format (excluding option: 9)

*.txt

fasta{:bash}

meta{:bash}

:map

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

${prefix}.fasta{:bash}

:file

Output in fasta format (only if —out_format 9)

*.fasta

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
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