Nextflow Registry | nf-core/antismash/antismashlite@0.0.0-6c4ed3a

nf-core/antismash/antismashlite @ 0.0.0-6c4ed3a

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters.

secondary metabolites BGC biosynthetic gene cluster genome mining NRPS RiPP antibiotics prokaryotes bacteria eukaryotes fungi antismash

Latest version: 0.0.0-6c4ed3a

Total downloads: 8

Source: nf-core/modules

Authors: @jasmezz

Maintainers: @jasmezz

Summary

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters.

Get started

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

include { ANTISMASH_ANTISMASHLITE } from 'nf-core/antismash/antismashlite'

License

MIT License

Process

`Name`	`ANTISMASH_ANTISMASHLITE`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`sequence_input` file	nucleotide sequence file (annotated) `*.{gbk, gb, gbff, genbank, embl, fasta, fna}`

`databases` directory	Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory "data/databases") `*/`

`antismash_dir` directory	A local copy of an AntiSMASH installation folder. This is required when running with docker and singularity (not required for conda), due to attempted 'modifications' of files during database checks in the installation directory, something that cannot be done in immutable docker/singularity containers. Therefore, a local installation directory needs to be mounted (including all modified files from the downloading step) to the container as a workaround. `*/`

antismash_dir directory

A local copy of an AntiSMASH installation folder. This is required when running with docker and singularity (not required for conda), due to attempted 'modifications' of files during database checks in the installation directory, something that cannot be done in immutable docker/singularity containers. Therefore, a local installation directory needs to be mounted (including all modified files from the downloading step) to the container as a workaround.

*/

Output 17 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.log` file	Contains all the logging output that antiSMASH produced during its run `*.log`

#2 zip tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.zip` file	Contains a compressed version of the output folder in zip format `*.zip`

#3 html tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/index.html` file	Graphical web view of results in HTML format

#4 gbk_input tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.gbk` file	Nucleotide sequence and annotations in GenBank format; converted from input file `*.gbk`

#5 gbk_results tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/region.gbk` file	Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit `region.gbk`

#6 json_results tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/*.json` file	Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input) `*.json`

#7 json_sideloading tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/regions.js` file	Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation "Annotation sideloading") `regions.js`

#8 clusterblast_file tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/clusterblast/_c.txt` file	Output of ClusterBlast algorithm `clusterblast/_c.txt`

#9 clusterblastoutput tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/clusterblastoutput.txt` file	Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm `c`