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55 lines
1.6 KiB
YAML
55 lines
1.6 KiB
YAML
name: mobsuite_recon
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description: A tool to reconstruct plasmids in bacterial assemblies
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keywords:
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- bacteria
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- plasmid
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tools:
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- mobsuite:
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description: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
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homepage: https://github.com/phac-nml/mob-suite
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documentation: https://github.com/phac-nml/mob-suite
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tool_dev_url: https://github.com/phac-nml/mob-suite
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doi: "10.1099/mgen.0.000435"
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licence: ["Apache License, Version 2.0"]
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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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- fasta:
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type: file
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description: A bacterial genome assembly in FASTA format
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pattern: "*.{fasta,fa,fna}"
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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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- chromosome:
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type: file
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description: FASTA file of all contigs found to belong to the chromosome
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pattern: "chromosome.fasta"
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- contig_report:
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type: file
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description: Assignment of the contig to chromosome or a particular plasmid grouping
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pattern: "contig_report.txt"
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- plasmids:
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type: file
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description: Each plasmid group is written to an individual FASTA
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pattern: "plasmid_*.fasta"
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- mobtyper_results:
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type: file
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description: Aggregate MOB-typer report files for all identified plasmid
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pattern: "mobtyper_results.txt"
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authors:
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- "@rpetit3"
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