Nextflow Registry | nf-core/deepbgc/pipeline@0.0.0-6c4ed3a

nf-core/deepbgc/pipeline @ 0.0.0-6c4ed3a

DeepBGC detects BGCs in bacterial and fungal genomes using deep learning.

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @louperelo @jfy133

Maintainers: @louperelo @jfy133

DeepBGC detects BGCs in bacterial and fungal genomes using deep learning.

Add the following snippet to your workflow script to include this module.

include { DEEPBGC_PIPELINE } from 'nf-core/deepbgc/pipeline'

MIT License

Process

`Name`	`DEEPBGC_PIPELINE`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`genome` file	FASTA/GenBank/Pfam CSV file `*.{fasta,fa,fna,gbk,csv}`

`db` directory	Database path

Output 13 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/LOG.txt` file	Log output of DeepBGC `*.{txt}`

#2 json tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/${prefix}.antismash.json` file	AntiSMASH JSON file for sideloading `*.{json}`

#3 pr_png tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/evaluation/${prefix}.pr.png` file	Precision-Recall curve based on predicted per-Pfam BGC scores `*.{pr.png}`

#4 readme tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/README.txt` file	txt file containing description of output files `*.{txt}`

#5 bgc_gbk tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/${prefix}.bgc.gbk` file	Sequences and features of all detected BGCs in GenBank format `*.{bgc.gbk}`

#6 bgc_png tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/evaluation/${prefix}.bgc.png` file	Detected BGCs plotted by their nucleotide coordinates `*.{bgc.png}`

#7 bgc_tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/${prefix}.bgc.tsv` file	Table of detected BGCs and their properties `*.{bgc.tsv}`

#8 roc_png tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/evaluation/${prefix}.roc.png` file	ROC curve based on predicted per-Pfam BGC scores `*.{roc.png}`

#9 full_gbk tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/${prefix}.full.gbk` file	Fully annotated input sequence with proteins, Pfam domains (PFAM_domain features) and BGCs (cluster features) `*.{full.gbk}`

#10 pfam_tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test']
`${prefix}/${prefix}.pfam.tsv` file	Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores `*.{pfam.tsv}`

#11 score_png tuple