name: "canu"
description: Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads.
keywords:
  - Assembly
  - pacbio
  - hifi
  - nanopore
tools:
  - "canu":
      description: "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing."
      homepage: "https://canu.readthedocs.io/en/latest/index.html#"
      documentation: "https://canu.readthedocs.io/en/latest/tutorial.html"
      tool_dev_url: "https://github.com/marbl/canu"
      doi: "10.1101/gr.215087.116"
      licence: "['GPL v2 and others']"
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:true ]
  - reads:
      type: file
      description: fasta/fastq file
      pattern: "*.{fasta,fastq}"
  - mode:
      type: value
      description: Canu mode depending on the input data (source and error rate)
      pattern: "-pacbio|-nanopore|-pacbio-hifi"
  - genomesize:
      type: value
      description: An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g
      pattern: "<number>[g|m|k]"
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"
  - report:
      type: file
      description: Most of the analysis reported during assembly
      pattern: "*.report"
  - assembly:
      type: file
      description: Everything which could be assembled and is the full assembly, including both unique, repetitive, and bubble elements.
      pattern: "*.contigs.fasta"
  - contigs:
      type: file
      description: Reads and low-coverage contigs which could not be incorporated into the primary assembly.
      pattern: "*.unassembled.fasta"
  - corrected_reads:
      type: file
      description: The reads after correction.
      pattern: "*.correctedReads.fasta.gz"
  - corrected_trimmed_reads:
      type: file
      description: The corrected reads after overlap based trimming
      pattern: "*.trimmedReads.fasta.gz"
  - metadata:
      type: file
      description: (undocumented)
      pattern: "*.contigs.layout"
  - contig_position:
      type: file
      description: The position of each read in a contig
      pattern: "*.contigs.layout.readToTig"
  - contig_info:
      type: file
      description: A list of the contigs, lengths, coverage, number of reads and other metadata. Essentially the same information provided in the FASTA header line.
      pattern: "*.contigs.layout.tigInfo"
authors:
  - "@scorreard"
maintainers:
  - "@scorreard"
