Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

sequence_input{:bash}

:file

nucleotide sequence file (annotated)

*.{gbk, gb, gbff, genbank, embl, fasta, fna}

databases{:bash}

:directory

Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory “data/databases”)

*/

antismash_dir{:bash}

: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{:bash}

meta{:bash}

:map

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

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

:directory

Accessory files for the HTML output

{css/,images/,js/}

gbk_input{:bash}

meta{:bash}

:map

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

${prefix}/*.gbk{:bash}

:file

Nucleotide sequence and annotations in GenBank format; converted from input file

*.gbk

json_results{:bash}

meta{:bash}

:map

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

${prefix}/*.json{:bash}

:file

Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)

*.json

log{:bash}

meta{:bash}

:map

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

${prefix}/*.log{:bash}

:file

Contains all the logging output that antiSMASH produced during its run

*.log

zip{:bash}

meta{:bash}

:map

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

${prefix}/*.zip{:bash}

:file

Contains a compressed version of the output folder in zip format

*.zip

html{:bash}

meta{:bash}

:map

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

${prefix}/index.html{:bash}

:file

Graphical web view of results in HTML format

json_sideloading{:bash}

meta{:bash}

:map

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

${prefix}/regions.js{:bash}

:file

Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation “Annotation sideloading”)

regions.js

clusterblast_file{:bash}

meta{:bash}

:map

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

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

:file

Output of ClusterBlast algorithm

clusterblast/*_c*.txt

knownclusterblast_html{:bash}

meta{:bash}

:map

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

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

:file

Tables with MIBiG hits in HTML format

knownclusterblast/region*/ctg*.html

knownclusterblast_dir{:bash}

meta{:bash}

:map

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

${prefix}/knownclusterblast/{:bash}

:directory

Directory with MIBiG hits

knownclusterblast/

knownclusterblast_txt{:bash}

meta{:bash}

:map

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

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

:file

Tables with MIBiG hits

knownclusterblast/*_c*.txt

svg_files_clusterblast{:bash}

meta{:bash}

:map

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

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

:file

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

svg/clusterblast*.svg

svg_files_knownclusterblast{:bash}

meta{:bash}

:map

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

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

:file

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

svg/knownclusterblast*.svg

gbk_results{:bash}

meta{:bash}

:map

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

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

:file

Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit

*region*.gbk

clusterblastoutput{:bash}

meta{:bash}

:map

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

${prefix}/clusterblastoutput.txt{:bash}

:file

Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm

clusterblastoutput.txt

knownclusterblastoutput{:bash}

meta{:bash}

:map

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

${prefix}/knownclusterblastoutput.txt{:bash}

:file

Raw BLAST output of known clusters of the MIBiG database

knownclusterblastoutput.txt

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

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
maintainer
Github user jasmezz
get in touch
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