Assess the quality of metagenome-assembled viral genomes.
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
fasta file
*.{fasta,fna,fa}
db{:bash}
:directory
Directory pointing to checkV database
Output
name:type
description
pattern
quality_summary{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/quality_summary.tsv{:bash}
: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{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/completeness.tsv{:bash}
:file
CheckV’s detailed overview table on estimating completeness
${prefix}/completeness.tsv
contamination{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/contamination.tsv{:bash}
:file
CheckV’s detailed overview table on estimating contamination
${prefix}/contamination.tsv
complete_genomes{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/complete_genomes.tsv{:bash}
:file
CheckV’s detailed overview table on the identified putative complete genomes
${prefix}/complete_genomes.tsv
proviruses{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/proviruses.fna{:bash}
:file
CheckV’s extracted proviruses contigs
${prefix}/proviruses.fna
viruses{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘sample’, bin:‘1’ ]
${prefix}/viruses.fna{:bash}
:file
CheckV’s extracted virus contigs
${prefix}/viruses.fna
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
checkv
BSD License
Assess the quality of metagenome-assembled viral genomes.
