Assess the quality of metagenome-assembled viral genomes.
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fasta
:file
fasta file
*.{fasta,fna,fa}
db
:directory
Directory pointing to checkV database
Output
name:type
description
pattern
quality_summary
meta
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/quality_summary.tsv
:file
CheckV’s main output containing integrated results from the three main modules (contamination, completeness, complete genomes) with overall quality of contigs
${prefix}/quality_summary.tsv
completeness
meta
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/completeness.tsv
:file
CheckV’s detailed overview table on estimating completeness
${prefix}/completeness.tsv
contamination
meta
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/contamination.tsv
:file
CheckV’s detailed overview table on estimating contamination
${prefix}/contamination.tsv
complete_genomes
meta
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/complete_genomes.tsv
:file
CheckV’s detailed overview table on the identified putative complete genomes
${prefix}/complete_genomes.tsv
proviruses
meta
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/proviruses.fna
:file
CheckV’s extracted proviruses contigs
${prefix}/proviruses.fna
viruses
meta
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/viruses.fna
:file
CheckV’s extracted virus contigs
${prefix}/viruses.fna
versions_checkv
${task.process}
:string
The name of the process
checkv
:string
The name of the tool
checkv -h 2>&1 | sed '1!d;s/^.*CheckV 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
checkv
:string
The name of the tool
checkv -h 2>&1 | sed '1!d;s/^.*CheckV v//;s/:.*//'
:eval
The expression to obtain the version of the tool
Tools
checkv
BSD License
Assess the quality of metagenome-assembled viral genomes.
