Assembles bacterial genomes
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
shortreads{:bash}
:file
List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
longreads{:bash}
List of input FastQ files of size 1, PacBio or Nanopore long reads.
scaffolds{:bash}
*.scaffolds.fa.gz{:bash}
Fasta file containing scaffolds
*.{scaffolds.fa.gz}
gfa{:bash}
*.assembly.gfa.gz{:bash}
gfa file containing assembly
*.{assembly.gfa.gz}
log{:bash}
*.log{:bash}
unicycler log file
*.{log}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Hybrid assembly pipeline for bacterial genomes
