name: spades
description: Assembles a small genome (bacterial, fungal, viral)
keywords:
  - genome
  - assembly
  - genome assembler
  - small genome
  - de novo assembler
tools:
  - spades:
      description: SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
      homepage: http://cab.spbu.ru/files/release3.15.0/manual.html
      documentation: http://cab.spbu.ru/files/release3.15.0/manual.html
      tool_dev_url: https://github.com/ablab/spades
      doi: 10.1089/cmb.2012.0021
      licence: ['GPL v2']
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - illumina:
      type: file
      description: |
        List of input FastQ (Illumina or PacBio CCS reads) files
        of size 1 and 2 for single-end and paired-end data,
        respectively. This input data type is required.
  - pacbio:
      type: file
      description: |
        List of input PacBio CLR FastQ files of size 1.
  - nanopore:
      type: file
      description: |
        List of input FastQ files of size 1, originating from Oxford Nanopore technology.
  - hmm:
      type: file
      description:
        File or directory with amino acid HMMs for Spades HMM-guided mode.
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - scaffolds:
      type: file
      description: |
        Fasta file containing scaffolds
      pattern: "*.fa.gz"
  - contigs:
      type: file
      description: |
        Fasta file containing contigs
      pattern: "*.fa.gz"
  - transcripts:
      type: file
      description: |
        Fasta file containing transcripts
      pattern: "*.fa.gz"
  - gene_clusters:
      type: file
      description: |
        Fasta file containing gene_clusters
      pattern: "*.fa.gz"
  - gfa:
      type: file
      description: |
        gfa file containing assembly
      pattern: "*.gfa.gz"
  - log:
      type: file
      description: |
        Spades log file
      pattern: "*.log"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@JoseEspinosa"
  - "@drpatelh"
  - "@d4straub"