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68 lines
1.9 KiB
YAML
68 lines
1.9 KiB
YAML
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name: checkm_qa
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description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
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keywords:
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- checkm
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- mag
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- metagenome
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- quality
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- isolates
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- microbes
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- single cells
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- completeness
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- contamination
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- bins
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- genome bins
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- qa
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- quality assurnce
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tools:
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- checkm:
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description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
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homepage: https://ecogenomics.github.io/CheckM/
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documentation: https://github.com/Ecogenomics/CheckM/wiki
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tool_dev_url: https://github.com/Ecogenomics/CheckM
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doi: "10.1101/gr.186072.114"
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licence: ["GPL v3"]
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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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- analysis_dir:
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type: file
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description: Directory containing output of checkm/analyze or checkm/lineage_wf etc.
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pattern: "*"
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- marker_file:
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type: file
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description: Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf
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pattern: "*.ms"
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- coverage_file:
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type: file
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description: File containing coverage of each sequence (generated by checkm coverage)
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- exclude_marker_file:
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type: file
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description: File specifying markers to exclude from marker sets
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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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- output:
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type: file
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description: "Default completeness statistics in various formats, as specified with --out_format (excluding option: 9)"
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pattern: "*.txt"
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- fasta:
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type: file
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description: Output in fasta format (only if --out_format 9)
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pattern: "*.fasta"
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authors:
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- "@jfy133"
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