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102 lines
3 KiB
YAML
102 lines
3 KiB
YAML
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name: "merqury"
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description: k-mer based assembly evaluation.
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keywords:
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- "k-mer"
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- "assembly"
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- "evaluation"
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tools:
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- "merqury":
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description: "Evaluate genome assemblies with k-mers and more."
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homepage: "None"
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documentation: "None"
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tool_dev_url: "https://github.com/marbl/merqury"
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doi: "10.1186/s13059-020-02134-9"
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licence: "['PUBLIC DOMAIN']"
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- meryl_db:
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type: file
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description: "Meryl read database"
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- assembly:
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type: file
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description: FASTA assembly file
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- assembly_only_kmers_bed:
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type: file
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description: "The positions of the k-mers found only in an assembly for further investigation in .bed"
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pattern: "*_only.bed"
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- assembly_only_kmers_wig:
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type: file
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description: "The positions of the k-mers found only in an assembly for further investigation in .wig"
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pattern: "*_only.wig"
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- stats:
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type: file
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description: Assembly statistics file
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pattern: "*.completeness.stats"
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- dist_hist:
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type: file
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description: Histogram
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pattern: "*.dist_only.hist"
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- spectra_cn_fl_png:
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type: file
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description: "Unstacked copy number spectra filled plot in PNG format"
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pattern: "*.spectra-cn.fl.png"
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- spectra_cn_ln_png:
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type: file
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description: "Unstacked copy number spectra line plot in PNG format"
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pattern: "*.spectra-cn.ln.png"
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- spectra_cn_st_png:
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type: file
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description: "Stacked copy number spectra line plot in PNG format"
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pattern: "*.spectra-cn.st.png"
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- spectra_cn_hist:
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type: file
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description: "Copy number spectra histogram"
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pattern: "*.spectra-cn.hist"
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- spectra_asm_fl_png:
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type: file
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description: "Unstacked assembly spectra filled plot in PNG format"
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pattern: "*.spectra-asm.fl.png"
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- spectra_asm_ln_png:
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type: file
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description: "Unstacked assembly spectra line plot in PNG format"
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pattern: "*.spectra-asm.ln.png"
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- spectra_asm_st_png:
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type: file
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description: "Stacked assembly spectra line plot in PNG format"
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pattern: "*.spectra-asm.st.png"
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- spectra_asm_hist:
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type: file
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description: "Assembly spectra histogram"
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pattern: "*.spectra-asm.hist"
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- assembly_qv:
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type: file
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description: "Assembly consensus quality estimation"
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pattern: "*.qv"
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- scaffold_qv:
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type: file
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description: "Scaffold consensus quality estimation"
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pattern: "*.qv"
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- read_ploidy:
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type: file
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description: "Ploidy estimate from read k-mer database"
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pattern: "*.hist.ploidy"
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authors:
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- "@mahesh-panchal"
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