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eae945721d
* not working yet (db not found)
* modify deeparg/download module to return db-path
* 🪄
* Prettier
* add test.yml
* much prettier
* test.yml delete md5 for pot. empty files
* adapt test.yml
* test.yml again
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
88 lines
2.5 KiB
YAML
88 lines
2.5 KiB
YAML
name: "deepbgc_pipeline"
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description: detect BGCs in bacterial and fungal genomes using deep learning
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keywords:
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- Biosynthetic Gene Cluster
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- deep learning
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- neural network
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- random forest
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- genomes
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- bacteria
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- fungi
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tools:
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- "deepbgc":
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description: "DeepBGC - Biosynthetic Gene Cluster detection and classification"
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homepage: "https://github.com/Merck/deepbgc"
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documentation: "https://github.com/Merck/deepbgc"
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tool_dev_url: "https://github.com/Merck/deepbgc"
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doi: "10.1093/nar/gkz654"
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licence: "['MIT']"
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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' ]
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- genome:
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type: file
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description: FASTA/GenBank/Pfam CSV file
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pattern: "*.{fasta,fa,fna,gbk,csv}"
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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']
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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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- readme:
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type: file
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description: txt file containing description of output files
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pattern: "*.{txt}"
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- log:
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type: file
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description: Log output of DeepBGC
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pattern: "*.{txt}"
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- json:
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type: file
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description: AntiSMASH JSON file for sideloading.
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pattern: "*.{json}"
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- bgc_gbk:
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type: file
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description: Sequences and features of all detected BGCs in GenBank format.
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pattern: "*.{bgc.gbk}"
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- bgc_tsv:
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type: file
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description: Table of detected BGCs and their properties.
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pattern: "*.{bgc.tsv}"
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- full_gbk:
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type: file
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description: Fully annotated input sequence with proteins, Pfam domains (PFAM_domain features) and BGCs (cluster features)
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pattern: "*.{full.gbk}"
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- pfam_tsv:
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type: file
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description: Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores.
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pattern: "*.{pfam.tsv}"
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- bgc_png:
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type: file
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description: Detected BGCs plotted by their nucleotide coordinates.
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pattern: "*.{bgc.png}"
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- pr_png:
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type: file
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description: Precision-Recall curve based on predicted per-Pfam BGC scores.
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pattern: "*.{pr.png}"
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- roc_png:
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type: file
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description: ROC curve based on predicted per-Pfam BGC scores.
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pattern: "*.{roc.png}"
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- score_png:
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type: file
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description: BGC detection scores of each Pfam domain in genomic order.
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pattern: "*.{score.png}"
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authors:
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- "@louperelo"
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- "@jfy133"
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