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
]
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
versions.yml:file
File containing software versions
versions.yml
Tools
checkv
BSD License
Assess the quality of metagenome-assembled viral genomes.
