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48 lines
1.3 KiB
YAML
48 lines
1.3 KiB
YAML
name: "mash_screen"
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description: Screens query sequences against large sequence databases
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keywords:
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- screen
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- containment
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- contamination
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- taxonomic assignment
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tools:
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- "mash":
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description: Fast sequence distance estimator that uses MinHash
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homepage: https://github.com/marbl/Mash
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documentation: https://mash.readthedocs.io/en/latest/sketches.html
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tool_dev_url: https://github.com/marbl/Mash
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doi: "10.1186/s13059-016-0997-x"
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licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"]
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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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- query:
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type: file
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description: Query sequences
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pattern: "*.fastq.gz"
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- sequence_sketch:
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type: file
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description: Sequence files to match against
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pattern: "*.msh"
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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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- screen:
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type: file
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description: List of sequences from fastx_db similar to query sequences
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pattern: "*.screen"
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authors:
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- "@mahesh-panchal"
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