name: "flye"
description: De novo assembler for single molecule sequencing reads
keywords:
  - assembly
  - genome
  - de novo
  - genome assembler
  - single molecule
tools:
  - "flye":
      description: "Fast and accurate de novo assembler for single molecule sequencing reads"
      homepage: "https://github.com/fenderglass/Flye"
      documentation: "https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md"
      tool_dev_url: "https://github.com/fenderglass/Flye"
      doi: "10.1038/s41592-020-00971-x"
      licence: "['BSD-3-clause']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - reads:
      type: file
      description: Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format.
      pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}"
  - mode:
      type: value
      description: Flye mode depending on the input data (source and error rate)
      pattern: "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test' ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - fasta:
      type: file
      description: Assembled FASTA file
      pattern: "*.fasta.gz"
  - gfa:
      type: file
      description: Repeat graph in gfa format
      pattern: "*.gfa.gz"
  - gv:
      type: file
      description: Repeat graph in gv format
      pattern: "*.gv.gz"
  - txt:
      type: file
      description: Extra information and statistics about resulting contigs
      pattern: "*.txt"
  - log:
      type: file
      description: Flye log file
      pattern: "*.log"
  - json:
      type: file
      description: Flye parameters
      pattern: "*.json"

authors:
  - "@mirpedrol"