mirror of
https://github.com/MillironX/nf-core_modules.git
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daab0a77dd
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
60 lines
1.7 KiB
YAML
60 lines
1.7 KiB
YAML
name: hamronization_deeparg
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description: Tool to convert and summarize DeepARG outputs using the hAMRonization specification
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keywords:
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- amr
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- antimicrobial resistance
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- reporting
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- deeparg
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tools:
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- hamronization:
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description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification
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homepage: https://github.com/pha4ge/hAMRonization/
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documentation: https://github.com/pha4ge/hAMRonization/
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tool_dev_url: https://github.com/pha4ge/hAMRonization
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doi: ""
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licence: ["GNU Lesser General Public v3 (LGPL 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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- report:
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type: file
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description: Output .mapping.ARG file from DeepARG
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pattern: "*.mapping.ARG"
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- format:
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type: value
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description: Type of report file to be produced
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pattern: "tsv|json"
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- software_version:
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type: value
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description: Version of DeepARG used
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pattern: "[0-9].[0-9].[0-9]"
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- reference_db_version:
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type: value
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description: Database version of DeepARG used
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pattern: "[0-9]"
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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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- json:
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type: file
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description: hAMRonised report in JSON format
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pattern: "*.json"
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- tsv:
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type: file
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description: hAMRonised report in TSV format
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pattern: "*.json"
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authors:
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- "@jfy133"
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