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meta.yml
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meta.yml
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name: unicycler
description: Assembles bacterial genomes
keywords:
- genome
- assembly
- genome assembler
- small genome
tools:
- unicycler:
description: Hybrid assembly pipeline for bacterial genomes
homepage: https://github.com/rrwick/Unicycler
documentation: https://github.com/rrwick/Unicycler
tool_dev_url: https://github.com/rrwick/Unicycler
doi: 10.1371/journal.pcbi.1005595
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- shortreads:
type: file
description: |
List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
- longreads:
type: file
description: |
List of input FastQ files of size 1, PacBio or Nanopore long reads.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- scaffolds:
type: file
description: Fasta file containing scaffolds
pattern: "*.{scaffolds.fa.gz}"
- gfa:
type: file
description: gfa file containing assembly
pattern: "*.{assembly.gfa.gz}"
- log:
type: file
description: unicycler log file
pattern: "*.{log}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@JoseEspinosa"
- "@drpatelh"
- "@d4straub"