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