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9d7208504d
* Add gecco/run module * Fix container URLs * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
67 lines
2.1 KiB
YAML
67 lines
2.1 KiB
YAML
name: "gecco_run"
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description: GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).
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keywords:
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- bgc
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- detection
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- metagenomics
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- contigs
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tools:
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- "gecco":
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description: "Biosynthetic Gene Cluster prediction with Conditional Random Fields."
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homepage: "https://gecco.embl.de"
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documentation: "https://gecco.embl.de"
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tool_dev_url: "https://github.com/zellerlab/GECCO"
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doi: "10.1101/2021.05.03.442509"
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licence: "['GPL 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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- input:
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type: file
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description: A genomic file containing one or more sequences as input. Input type is any supported by Biopython (fasta, gbk, etc.)
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pattern: "*"
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- hmm:
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file: file
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description: Alternative HMM file(s) to use in HMMER format
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pattern: "*.hmm"
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- model_dir:
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file: directory
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description: Path to an alternative CRF (Conditional Random Fields) module to use
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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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- genes:
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type: file
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description: TSV file containing detected/predicted genes with BGC probability scores
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pattern: "*.genes.tsv"
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- features:
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type: file
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description: TSV file containing identified domains
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pattern: "*.features.tsv"
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- clusters:
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type: file
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description: TSV file containing coordinates of predicted clusters and BGC types
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pattern: "*.clusters.tsv"
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- gbk:
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type: file
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description: Per cluster GenBank file (if found) containing sequence with annotations
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pattern: "*.gbk"
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- json:
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type: file
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description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied
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pattern: "*.gbk"
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authors:
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- "@jfy133"
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