nf-core_modules/modules/merqury/meta.yml

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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"