Quality Assessment Tool for Genome Assemblies
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
consensus{:bash}
:file
Fasta file containing the assembly of interest
meta2{:bash}
fasta{:bash}
The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value.
meta3{:bash}
gff{:bash}
The genome GFF file. Has to contain at least a non-empty string dummy value.
results{:bash}
${prefix}{:bash}
:directory
Directory containing the results of the QUAST analysis
tsv{:bash}
${prefix}.tsv{:bash}
TSV file
${prefix}.tsv
transcriptome{:bash}
${prefix}_transcriptome.tsv{:bash}
Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided
${prefix}_transcriptome.tsv
misassemblies{:bash}
${prefix}_misassemblies.tsv{:bash}
Report containing misassemblies, only when a reference fasta is provided
${prefix}_misassemblies.tsv
unaligned{:bash}
${prefix}_unaligned.tsv{:bash}
Report containing unaligned contigs, only when a reference fasta is provided
${prefix}_unaligned.tsv
versions_quast{:bash}
${task.process}{:bash}
:string
The name of the process
quast{:bash}
The name of the tool
quast.py --version 2>&1 | grep "QUAST" | sed 's/^.*QUAST v//; s/ .*\$//'{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
QUAST calculates quality metrics for genome assemblies
