Nextflow Registry | nf-core/antismash/antismash@0.0.0-3fc6d40

nf-core/antismash/antismash @ 0.0.0-3fc6d40

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

Latest version: 0.0.0-3fc6d40

Total downloads: 7

Source: nf-core/modules

Authors: @jasmezz

Maintainers: @jasmezz @jfy133

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

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

include { ANTISMASH_ANTISMASH } from 'nf-core/antismash/antismash'

MIT License

Process

`Name`	`ANTISMASH_ANTISMASH`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test' ]
`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") `*/`

`gff` file	Optional GFF3 file containing premade annotations of the input sequence `*.gff`

Output 17 channels

#1 log tuple

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

#10 versions_antismash tuple