modules/checkm_qa

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

checkmmagmetagenomequalityisolatesmicrobessingle cellscompletenesscontaminationbinsgenome binsqaquality assurnce

https://github.com/nf-core/modules/[...]/modules/nf-core/checkm/qa

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:false ]

`analysis_dir`
`:file`

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

*

`marker_file`
`:file`

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

*.ms

`coverage_file`
`:file`

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

`exclude_marker_file`
`:file`

File specifying markers to exclude from marker sets

`db`
`:directory`

CheckM database directory

Output

name:type

description

pattern

`output`

`meta`
`:map`

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

`${prefix}.txt`
`:file`

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

*.txt

`fasta`

`meta`
`:map`

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

`${prefix}.fasta`
`:file`

Output in fasta format (only if —out_format 9)

*.fasta

`versions_checkm`

`${task.process}`
`:string`

The name of the process

`checkm`
`:string`

The name of the tool

`checkm 2>&1 | grep '...:::' | sed 's/.CheckM v//;s/ .//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`checkm`
`:string`

The name of the tool

`checkm 2>&1 | grep '...:::' | sed 's/.CheckM v//;s/ .//'`
`: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

modules/checkm_qa

Description

Input

`meta`
`:map`

`analysis_dir`
`:file`

`marker_file`
`:file`

`coverage_file`
`:file`

`exclude_marker_file`
`:file`

`db`
`:directory`

Output

`output`

`meta`
`:map`

`${prefix}.txt`
`:file`

`fasta`

`meta`
`:map`

`${prefix}.fasta`
`:file`

`versions_checkm`

`${task.process}`
`:string`

`checkm`
`:string`

`checkm 2>&1 | grep '...:::' | sed 's/.CheckM v//;s/ .//'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`checkm`
`:string`

`checkm 2>&1 | grep '...:::' | sed 's/.CheckM v//;s/ .//'`
`:eval`

Tools

checkm
GPL v3

included in

maintainer

get in touch

modules/checkm_qa

Description

Input

meta:map

analysis_dir:file

marker_file:file

coverage_file:file

exclude_marker_file:file

db:directory

Output

output

meta:map

${prefix}.txt:file

fasta

meta:map

${prefix}.fasta:file

versions_checkm

${task.process}:string

checkm:string

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

Topics

versions

${task.process}:string

checkm:string

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

Tools

checkm GPL v3

included in

maintainer

get in touch

`meta`
`:map`

`analysis_dir`
`:file`

`marker_file`
`:file`

`coverage_file`
`:file`

`exclude_marker_file`
`:file`

`db`
`:directory`

`output`

`meta`
`:map`

`${prefix}.txt`
`:file`

`fasta`

`meta`
`:map`

`${prefix}.fasta`
`:file`

`versions_checkm`

`${task.process}`
`:string`

`checkm`
`:string`

`checkm 2>&1 | grep '...:::' | sed 's/.CheckM v//;s/ .//'`
`:eval`

`versions`

`${task.process}`
`:string`

`checkm`
`:string`

`checkm 2>&1 | grep '...:::' | sed 's/.CheckM v//;s/ .//'`
`:eval`

checkm
GPL v3