modules/checkm_lineagewf

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

checkmmagmetagenomequalityisolatesmicrobessingle cellscompletenesscontaminationbinsgenome bins

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

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 ]

`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

`checkm_output`

`meta`
`:map`

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

`${prefix}`
`:directory`

CheckM output directory

*/

`marker_file`

`meta`
`:map`

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

`${prefix}/lineage.ms`
`:file`

Lineage file

*.ms

`checkm_tsv`

`meta`
`:map`

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

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

CheckM summary completeness statistics table

*.tsv

`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_lineagewf

Description

Input

`meta`
`:map`

`fasta`
`:file`

`fasta_ext`
`:string`

`db`
`:directory`

Output

`checkm_output`

`meta`
`:map`

`${prefix}`
`:directory`

`marker_file`

`meta`
`:map`

`${prefix}/lineage.ms`
`:file`

`checkm_tsv`

`meta`
`:map`

`${prefix}.tsv`
`: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_lineagewf

Description

Input

meta:map

fasta:file

fasta_ext:string

db:directory

Output

checkm_output

meta:map

${prefix}:directory

marker_file

meta:map

${prefix}/lineage.ms:file

checkm_tsv

meta:map

${prefix}.tsv: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`

`fasta`
`:file`

`fasta_ext`
`:string`

`db`
`:directory`

`checkm_output`

`meta`
`:map`

`${prefix}`
`:directory`

`marker_file`

`meta`
`:map`

`${prefix}/lineage.ms`
`:file`

`checkm_tsv`

`meta`
`:map`

`${prefix}.tsv`
`: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