mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
e55012ff92
* Fix variable prodigal_tf * Remove tag in main.nf + tiny suggestions in ymls Co-authored-by: louperelo <44900284+louperelo@users.noreply.github.com>
89 lines
2.6 KiB
YAML
89 lines
2.6 KiB
YAML
name: "deepbgc_pipeline"
|
|
description: DeepBGC detects BGCs in bacterial and fungal genomes using deep learning.
|
|
keywords:
|
|
- BGC
|
|
- biosynthetic gene cluster
|
|
- deep learning
|
|
- neural network
|
|
- random forest
|
|
- genomes
|
|
- bacteria
|
|
- fungi
|
|
tools:
|
|
- "deepbgc":
|
|
description: "DeepBGC - Biosynthetic Gene Cluster detection and classification"
|
|
homepage: "https://github.com/Merck/deepbgc"
|
|
documentation: "https://github.com/Merck/deepbgc"
|
|
tool_dev_url: "https://github.com/Merck/deepbgc"
|
|
doi: "10.1093/nar/gkz654"
|
|
licence: "['MIT']"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test' ]
|
|
- genome:
|
|
type: file
|
|
description: FASTA/GenBank/Pfam CSV file
|
|
pattern: "*.{fasta,fa,fna,gbk,csv}"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test']
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- readme:
|
|
type: file
|
|
description: txt file containing description of output files
|
|
pattern: "*.{txt}"
|
|
- log:
|
|
type: file
|
|
description: Log output of DeepBGC
|
|
pattern: "*.{txt}"
|
|
- json:
|
|
type: file
|
|
description: AntiSMASH JSON file for sideloading
|
|
pattern: "*.{json}"
|
|
- bgc_gbk:
|
|
type: file
|
|
description: Sequences and features of all detected BGCs in GenBank format
|
|
pattern: "*.{bgc.gbk}"
|
|
- bgc_tsv:
|
|
type: file
|
|
description: Table of detected BGCs and their properties
|
|
pattern: "*.{bgc.tsv}"
|
|
- full_gbk:
|
|
type: file
|
|
description: Fully annotated input sequence with proteins, Pfam domains (PFAM_domain features) and BGCs (cluster features)
|
|
pattern: "*.{full.gbk}"
|
|
- pfam_tsv:
|
|
type: file
|
|
description: Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores
|
|
pattern: "*.{pfam.tsv}"
|
|
- bgc_png:
|
|
type: file
|
|
description: Detected BGCs plotted by their nucleotide coordinates
|
|
pattern: "*.{bgc.png}"
|
|
- pr_png:
|
|
type: file
|
|
description: Precision-Recall curve based on predicted per-Pfam BGC scores
|
|
pattern: "*.{pr.png}"
|
|
- roc_png:
|
|
type: file
|
|
description: ROC curve based on predicted per-Pfam BGC scores
|
|
pattern: "*.{roc.png}"
|
|
- score_png:
|
|
type: file
|
|
description: BGC detection scores of each Pfam domain in genomic order
|
|
pattern: "*.{score.png}"
|
|
|
|
authors:
|
|
- "@louperelo"
|
|
- "@jfy133"
|