* add pre-formatted database info

* add information about pre-formatted database

* update version

* Add pre-formatted database (#83)

* add pre-formatted database info

* add information about pre-formatted database

* update falmeida-py package

* change version

* change main tools to public containers

* use biocontainer

* aggregate other non-biocontainer tools and diminish the size of docker images

* update module labels

* re-arranged docker images

* add integron_finder module

* update amrfinder version

* trying to addintegron finder to gff

* update docker

* fixed image install

* fixed integron finder 2 gff

* remove unnecessary grouptuple

* fix image and emboss module

* fix organization

* add docker image to module

* fix indentation

* fix indentation

* added integron finder results to final GFF and JBROWSE

* integron finder results added to HTML report

* fix docker image

* properly added to json summary

* update changelog

* update readme

* update list of tools

* update default config in docs

* backscape tildes

* update installation docs

* fix indentation

* update outputs docs

* fix wrong pipeline name

* fix typo

* update quickstart

* fixed mlst execution in singularity

* fix indentation

…r than 20 and not separated by tab or space (#89)

* add awk command to clean big fasta headers

* add awk statement to clean big fasta headers

* update bakta version

* Add pre-formatted database (#83)

* add pre-formatted database info

* add information about pre-formatted database

* add mob suite module

* added results to HTML report

* Update Dockerfile

* added mob_suite to json summary

* add tool to markdown files

* add tool information to docs

* add example reports

* include module to download pre-built databases

* update docs

* moved container configurations of assembly modules

* update default flye version

* update container configuration for database-setup modules

* re-organize container definition of 'generic' modules

* reorganize container configuration for KO modules

* reorganized container configuration for MGEs modules

* finalizing container configuration reorganization of last modules

* containers already defined in config files

* update params schema

* fixed zenodo download

* mob_suite singularity image not always suited for low connection servers

* add option to download container configs

Update falmeida-py version

* Try Dockerfile fix

* Update Dockerfile

* Update Dockerfile

* Update CHANGELOG.md

…108)

* fix singularity run options

* fix misc dockerfile

* update renv docker image environment

* update docker images to use shasum

* Update CHANGELOG.md

* Add pre-formatted database (#83)

* add pre-formatted database info

* add information about pre-formatted database

* update docs and fix report links

* include information of newly known issues (#103)

* add parameter to enable deduplication of reads

* Update manual.md

* update cli help

* Update installation.md

* add indentation

* Update README.md

* Update README.md

* fix tracedir

* always show from copy

* Update quickstart.md

* Update manual.md

* update for dev-testing

* adapt to antismash lite as the normal installation is horrible

* change for dev image

* updated docker image with stable 1.2.4 release of falmeida-py package for bugfix

* update changelog

add parameters to skip the INTEGRON_FINDER and CIRCOS modules when desired.

…aram

118 add skip integron finder param

… for singularity in order to avoid problems related to read-only filesystem that happens with this tool