modules/
antismash_antismashlitedownloaddatabases

antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs.

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

https://github.com/nf-core/modules/tree/master/modules/nf-core/antismash/antismashlitedownloaddatabases

Description

Input

Name

Description

Pattern

`database_css` (directory)

antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.

css

`database_detection` (directory)

antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.

detection

`database_modules` (directory)

antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.

modules