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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_abricate"
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description: Tool to convert and summarize ABRicate 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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- abricate
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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 TSV or CSV file from ABRicate
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pattern: "*.{csv,tsv}"
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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 ABRicate 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 ABRicate used
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pattern: "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][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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- "@jasmezz"
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