Assemble bacterial isolate genomes from Illumina paired-end reads
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
List of input paired-end FastQ files
contigs{:bash}
contigs.fa{:bash}
The final assembly produced by Shovill
contigs.fa
corrections{:bash}
shovill.corrections{:bash}
List of post-assembly corrections made by Shovill
shovill.corrections
log{:bash}
shovill.log{:bash}
Full log file for bug reporting
shovill.log
raw_contigs{:bash}
{skesa,spades,megahit,velvet}.fasta{:bash}
Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)
{skesa,spades,megahit,velvet}.fasta
gfa{:bash}
contigs.{fastg,gfa,LastGraph}{:bash}
Assembly graph produced by MEGAHIT, SPAdes, or Velvet
contigs.{fastg,gfa,LastGraph}
versions_shovill{:bash}
${task.process}{:bash}
:string
The name of the process
shovill{:bash}
The name of the tool
shovill --version 2>&1 | sed "s/^.*shovill //"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Microbial assembly pipeline for Illumina paired-end reads
