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b3acfc54f5
* Support non-GFF input * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Fix linting error Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
131 lines
4.5 KiB
YAML
131 lines
4.5 KiB
YAML
name: antismash_antismashlite
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description: |
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antiSMASH allows the rapid genome-wide identification, annotation
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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, fasta, fna}"
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- databases:
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type: directory
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description: |
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Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory
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"data/databases")
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pattern: "*/"
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- antismash_dir:
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type: directory
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description: |
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A local copy of an AntiSMASH installation folder. This is required when running with
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docker and singularity (not required for conda), due to attempted 'modifications' of
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files during database checks in the installation directory, something that cannot
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be done in immutable docker/singularity containers. Therefore, a local installation
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directory needs to be mounted (including all modified files from the downloading step)
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to the container as a workaround.
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pattern: "*/"
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- gff:
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type: file
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description: Annotations in GFF3 format (only if sequence_input is in FASTA format)
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pattern: "*.gff"
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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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- html_accessory_files:
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type: directory
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description: Accessory files for the HTML output
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pattern: "{css/,images/,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 images 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 images 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 and annotations in GenBank 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: Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)
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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 output 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 and annotations in GenBank 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 antiSMASH documentation "Annotation sideloading")
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pattern: "regions.js"
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authors:
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- "@jasmezz"
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