name: "merqury"
description: k-mer based assembly evaluation.
keywords:
  - "k-mer"
  - "assembly"
  - "evaluation"
tools:
  - "merqury":
      description: "Evaluate genome assemblies with k-mers and more."
      homepage: "None"
      documentation: "None"
      tool_dev_url: "https://github.com/marbl/merqury"
      doi: "10.1186/s13059-020-02134-9"
      licence: "['PUBLIC DOMAIN']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - meryl_db:
      type: file
      description: "Meryl read database"
  - assembly:
      type: file
      description: FASTA assembly file

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"
  - assembly_only_kmers_bed:
      type: file
      description: "The positions of the k-mers found only in an assembly for further investigation in .bed"
      pattern: "*_only.bed"
  - assembly_only_kmers_wig:
      type: file
      description: "The positions of the k-mers found only in an assembly for further investigation in .wig"
      pattern: "*_only.wig"
  - stats:
      type: file
      description: Assembly statistics file
      pattern: "*.completeness.stats"
  - dist_hist:
      type: file
      description: Histogram
      pattern: "*.dist_only.hist"
  - spectra_cn_fl_png:
      type: file
      description: "Unstacked copy number spectra filled plot in PNG format"
      pattern: "*.spectra-cn.fl.png"
  - spectra_cn_ln_png:
      type: file
      description: "Unstacked copy number spectra line plot in PNG format"
      pattern: "*.spectra-cn.ln.png"
  - spectra_cn_st_png:
      type: file
      description: "Stacked copy number spectra line plot in PNG format"
      pattern: "*.spectra-cn.st.png"
  - spectra_cn_hist:
      type: file
      description: "Copy number spectra histogram"
      pattern: "*.spectra-cn.hist"
  - spectra_asm_fl_png:
      type: file
      description: "Unstacked assembly spectra filled plot in PNG format"
      pattern: "*.spectra-asm.fl.png"
  - spectra_asm_ln_png:
      type: file
      description: "Unstacked assembly spectra line plot in PNG format"
      pattern: "*.spectra-asm.ln.png"
  - spectra_asm_st_png:
      type: file
      description: "Stacked assembly spectra line plot in PNG format"
      pattern: "*.spectra-asm.st.png"
  - spectra_asm_hist:
      type: file
      description: "Assembly spectra histogram"
      pattern: "*.spectra-asm.hist"
  - assembly_qv:
      type: file
      description: "Assembly consensus quality estimation"
      pattern: "*.qv"
  - scaffold_qv:
      type: file
      description: "Scaffold consensus quality estimation"
      pattern: "*.qv"
  - read_ploidy:
      type: file
      description: "Ploidy estimate from read k-mer database"
      pattern: "*.hist.ploidy"

authors:
  - "@mahesh-panchal"