Wrap-up v3.3 for release #93
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* 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
* 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
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