modules/antismash_antismashlite

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

secondary metabolitesBGCbiosynthetic gene clustergenome miningNRPSRiPPantibioticsprokaryotesbacteriaeukaryotesfungiantismash

https://github.com/nf-core/modules/[...]/modules/nf-core/antismash/antismashlite

This module is deprecated.

Description

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

Input

name:type

description

pattern

`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.

*/

Output

name:type

description

pattern

`html_accessory_files`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/{css,images,js}`
`:directory`

Accessory files for the HTML output

{css/,images/,js/}

`gbk_input`

`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

`json_results`

`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

`log`

`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

`zip`

`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

`html`

`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

`json_sideloading`

`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

`clusterblast_file`

`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

`knownclusterblast_html`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/knownclusterblast/region/ctg.html`
`:file`

Tables with MIBiG hits in HTML format

knownclusterblast/region*/ctg*.html

`knownclusterblast_dir`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/knownclusterblast/`
`:directory`

Directory with MIBiG hits

knownclusterblast/

`knownclusterblast_txt`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/knownclusterblast/_c.txt`
`:file`

Tables with MIBiG hits

knownclusterblast/*_c*.txt

`svg_files_clusterblast`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/svg/clusterblast*.svg`
`:file`

SVG images showing the % identity of the aligned hits against their queries

svg/clusterblast*.svg

`svg_files_knownclusterblast`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/svg/knownclusterblast*.svg`
`:file`

SVG images showing the % identity of the aligned hits against their queries

svg/knownclusterblast*.svg

`gbk_results`

`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

`clusterblastoutput`

`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

clusterblastoutput.txt

`knownclusterblastoutput`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${prefix}/knownclusterblastoutput.txt`
`:file`

Raw BLAST output of known clusters of the MIBiG database

knownclusterblastoutput.txt

`versions_antismash`

`${task.process}`
`:string`

The name of the process

`antismash-lite`
`:string`

The name of the tool

`antismash --version | sed 's/antiSMASH //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`antismash-lite`
`:string`

The name of the tool

`antismash --version | sed 's/antiSMASH //'`
`:eval`

The expression to obtain the version of the tool

Tools

antismashlite
AGPL v3

antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell

docs.antismash.secondarymetabolites.org https://github.com/antismash/antismash 10.1093/nar/gkab335

modules/antismash_antismashlite

Description

Input

meta:map

sequence_input:file

databases:directory

antismash_dir:directory

Output

html_accessory_files

meta:map

${prefix}/{css,images,js}:directory

gbk_input

meta:map

${prefix}/*.gbk:file

json_results

meta:map

${prefix}/*.json:file

log

meta:map

${prefix}/*.log:file

zip

meta:map

${prefix}/*.zip:file

html

meta:map

${prefix}/index.html:file

json_sideloading

meta:map

${prefix}/regions.js:file

clusterblast_file

meta:map

${prefix}/clusterblast/*_c*.txt:file

knownclusterblast_html

meta:map

${prefix}/knownclusterblast/region*/ctg*.html:file

knownclusterblast_dir

meta:map

${prefix}/knownclusterblast/:directory

knownclusterblast_txt

meta:map

${prefix}/knownclusterblast/*_c*.txt:file

svg_files_clusterblast

meta:map

${prefix}/svg/clusterblast*.svg:file

svg_files_knownclusterblast

meta:map

${prefix}/svg/knownclusterblast*.svg:file

gbk_results

meta:map

${prefix}/*region*.gbk:file

clusterblastoutput

meta:map

${prefix}/clusterblastoutput.txt:file

knownclusterblastoutput

meta:map

${prefix}/knownclusterblastoutput.txt:file

versions_antismash

${task.process}:string

antismash-lite:string

antismash --version | sed 's/antiSMASH //':eval

Topics

versions

${task.process}:string

antismash-lite:string

antismash --version | sed 's/antiSMASH //':eval

Tools

antismashlite AGPL v3

maintainer

get in touch

`meta`
`:map`

`sequence_input`
`:file`

`databases`
`:directory`

`antismash_dir`
`:directory`

`html_accessory_files`

`meta`
`:map`

`${prefix}/{css,images,js}`
`:directory`

`gbk_input`

`meta`
`:map`

`${prefix}/*.gbk`
`:file`

`json_results`

`meta`
`:map`

`${prefix}/*.json`
`:file`

`log`

`meta`
`:map`

`${prefix}/*.log`
`:file`

`zip`

`meta`
`:map`

`${prefix}/*.zip`
`:file`

`html`

`meta`
`:map`

`${prefix}/index.html`
`:file`

`json_sideloading`

`meta`
`:map`

`${prefix}/regions.js`
`:file`

`clusterblast_file`

`meta`
`:map`

`${prefix}/clusterblast/_c.txt`
`:file`

`knownclusterblast_html`

`meta`
`:map`

`${prefix}/knownclusterblast/region/ctg.html`
`:file`

`knownclusterblast_dir`

`meta`
`:map`

`${prefix}/knownclusterblast/`
`:directory`

`knownclusterblast_txt`

`meta`
`:map`

`${prefix}/knownclusterblast/_c.txt`
`:file`

`svg_files_clusterblast`

`meta`
`:map`

`${prefix}/svg/clusterblast*.svg`
`:file`

`svg_files_knownclusterblast`

`meta`
`:map`

`${prefix}/svg/knownclusterblast*.svg`
`:file`

`gbk_results`

`meta`
`:map`

`${prefix}/region.gbk`
`:file`

`clusterblastoutput`

`meta`
`:map`

`${prefix}/clusterblastoutput.txt`
`:file`

`knownclusterblastoutput`

`meta`
`:map`

`${prefix}/knownclusterblastoutput.txt`
`:file`

`versions_antismash`

`${task.process}`
`:string`

`antismash-lite`
`:string`

`antismash --version | sed 's/antiSMASH //'`
`:eval`

`versions`

`${task.process}`
`:string`

`antismash-lite`
`:string`

`antismash --version | sed 's/antiSMASH //'`
`:eval`

antismashlite
AGPL v3