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171a2a2dbf
* Unicycler with long read input * tests and md5sums * remove unstable md5sums * Update modules/unicycler/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
60 lines
1.6 KiB
YAML
60 lines
1.6 KiB
YAML
name: unicycler
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description: Assembles bacterial genomes
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keywords:
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- genome
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- assembly
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- genome assembler
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- small genome
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tools:
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- unicycler:
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description: Hybrid assembly pipeline for bacterial genomes
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homepage: https://github.com/rrwick/Unicycler
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documentation: https://github.com/rrwick/Unicycler
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tool_dev_url: https://github.com/rrwick/Unicycler
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doi: 10.1371/journal.pcbi.1005595
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licence: ['GPL v3']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- shortreads:
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type: file
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description: |
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List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- longreads:
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type: file
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description: |
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List of input FastQ files of size 1, PacBio or Nanopore long reads.
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- scaffolds:
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type: file
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description: Fasta file containing scaffolds
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pattern: "*.{scaffolds.fa.gz}"
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- gfa:
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type: file
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description: gfa file containing assembly
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pattern: "*.{assembly.gfa.gz}"
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- log:
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type: file
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description: unicycler log file
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pattern: "*.{log}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@JoseEspinosa"
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- "@drpatelh"
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- "@d4straub"
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