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61e740f79c
* Add missing container folders as output channels * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tool name * Update test output checksum Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
70 lines
4.4 KiB
YAML
70 lines
4.4 KiB
YAML
name: antismash_antismashlitedownloaddatabases
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description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases.
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keywords:
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- secondary metabolites
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- BGC
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- biosynthetic gene cluster
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- genome mining
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- NRPS
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- RiPP
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- antibiotics
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- prokaryotes
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- bacteria
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- eukaryotes
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- fungi
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- antismash
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- database
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tools:
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- antismash:
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description: antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell
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homepage: https://docs.antismash.secondarymetabolites.org
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documentation: https://docs.antismash.secondarymetabolites.org
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tool_dev_url: https://github.com/antismash/antismash
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doi: "10.1093/nar/gkab335"
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licence: ["AGPL v3"]
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input:
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- database_css:
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type: directory
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description: |
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antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "css"
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- database_detection:
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type: directory
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description: |
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antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "detection"
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- database_modules:
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type: directory
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description: |
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antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "modules"
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output:
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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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- database:
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type: directory
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description: Download directory for antiSMASH databases
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pattern: "antismash_db"
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- css_dir:
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type: directory
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description: |
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antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "css"
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- detection_dir:
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type: directory
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description: |
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antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "detection"
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- modules_dir:
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type: directory
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description: |
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antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "modules"
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authors:
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- "@jasmezz"
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