mirror of
https://github.com/MillironX/nf-core_modules.git
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122 lines
3.9 KiB
YAML
122 lines
3.9 KiB
YAML
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name: antismash_antismashlite
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description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters.
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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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tools:
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- antismashlite:
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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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- 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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- sequence_input:
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type: file
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description: nucleotide sequence file (annotated)
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pattern: "*.{gbk, gb, gbff, genbank, embl}"
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- databases:
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type: directory
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description: downloaded antismash databases e.g. data/databases
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pattern: "*"
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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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- clusterblast_file:
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type: file
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description: Output of ClusterBlast algorithm
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pattern: "clusterblast/*_c*.txt"
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- css_file:
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type: file
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description: Style sheet containing the formatting of HTML output
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pattern: "css/*.css"
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- image_directory:
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type: directory
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description: image files for web view of antiSMASH results
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pattern: "images"
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- javascript:
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type: file
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description: JavaScript files
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pattern: "js/*.js"
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- knownclusterblast_html:
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type: file
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description: Tables with MIBiG hits in HTML format
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pattern: "knownclusterblast/region*/ctg*.html"
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- knownclusterblast_txt:
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type: file
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description: Tables with MIBiG hits
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pattern: "knownclusterblast/*_c*.txt"
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- svg_files_clusterblast:
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type: file
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description: SVG image showing the % identity of the aligned hits against their queries
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pattern: "svg/clusterblast*.svg"
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- svg_files_knownclusterblast:
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type: file
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description: SVG image showing the % identity of the aligned hits against their queries
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pattern: "svg/knownclusterblast*.svg"
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- gbk_input:
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type: file
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description: Nucleotide sequence + annotations in GenBank file format; converted from input file
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pattern: "*.gbk"
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- json_results:
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type: file
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description: Simple representation of all detected areas during the antiSMASH run in JSON format
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pattern: "*.json"
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- log:
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type: file
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description: Contains all the logging output that antiSMASH produced during its run
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pattern: "*.log"
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- zip:
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type: file
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description: Contains a compressed version of the folder in zip format
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pattern: "*.zip"
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- gbk_results:
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type: file
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description: Nucleotide sequence + annotations in GenBank file format; one file per antiSMASH hit
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pattern: "*region*.gbk"
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- clusterblastoutput:
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type: file
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description: Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm
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pattern: "clusterblastoutput.txt"
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- html:
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type: file
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description: Graphical web view of results in HTML format
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patterN: "index.html"
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- knownclusterblastoutput:
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type: file
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description: Raw BLAST output of known clusters of the MIBiG database
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pattern: "knownclusterblastoutput.txt"
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- json_sideloading:
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type: file
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description: Sideloaded annotations of protoclusters and/or subregions (see documentation "Annotation sideloading")
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pattern: "regions.js"
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authors:
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- "@jasmezz"
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