name: megahit
description: An ultra-fast metagenomic assembler for large and complex metagenomics
keywords:
  - megahit
  - denovo
  - assembly
  - debruijn
  - metagenomics
tools:
  - megahit:
      description: "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"
      homepage: https://github.com/voutcn/megahit
      documentation: https://github.com/voutcn/megahit
      tool_dev_url: https://github.com/voutcn/megahit
      doi: "10.1093/bioinformatics/btv033"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed)
        e.g. [ id:'test', single_end:false ]
  - reads:
      type: file
      description: |
        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
        respectively in gzipped or uncompressed FASTQ or FASTA format.

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"
  - contigs:
      type: file
      description: Final final contigs result of the assembly in FASTA format.
      pattern: "*.contigs.fa.gz"
  - k_contigs:
      type: file
      description: Contigs assembled from the de Bruijn graph of order-K
      pattern: "k*.contigs.fa.gz"
  - addi_contigs:
      type: file
      description: Contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K
      pattern: "k*.addi.fa.gz"
  - local_contigs:
      type: file
      description: Contigs of the locally assembled contigs for k=K
      pattern: "k*.local.fa.gz"
  - kfinal_contigs:
      type: file
      description: Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty
      pattern: "k*.final.contigs.fa.gz"

authors:
  - "@jfy133"