Add pre-formatted database #82
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fmalmeida
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Oct 1, 2023
* Add pre-formatted database (#82) * add pre-formatted database info * add information about pre-formatted database * 50 add tool integron finder 20 (#87) * 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 * 85 prokka module can get after modules stuck if the header file longer 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 * fix bakta stats parsing * 81 add tool mob suite (#90) * 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 * update singularity config * fixed kofamscan download * fix dockerfile * Fix unicycler tag * use only docker images to avoid timeout error * use docker ocntainer to avoid singularity timeout * fixed resfinder for singularity * fixed docker image * fix gff2sql in singularity * use proper singularity images * fix singularity image download * fixed docker image * Add option for prebuilt db download (#94) * include module to download pre-built databases * update docs * 69 tools to use own docker image (#91) * 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 unicycler version (0.5.0--py310h6cc9453_3) * 96 error summary for bugfix release (#101) Update falmeida-py version * 98 include ices and prophage annotation in json summary (#106) * Try Dockerfile fix * Update Dockerfile * Update Dockerfile * Update CHANGELOG.md * 100 update pipeline docker images from docker tags to docker shasum (#108) * fix singularity run options * fix misc dockerfile * update renv docker image environment * update docker images to use shasum * Update CHANGELOG.md * 107 duplicate reads to unique read names (#109) * 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 changelog * Update docs for v3.3 (#110) * 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 citation information * add citation example * Update CHANGELOG.md
fmalmeida
added a commit
that referenced
this pull request
Oct 29, 2023
* Add pre-formatted database (#82) * add pre-formatted database info * add information about pre-formatted database * 50 add tool integron finder 20 (#87) * 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 * 85 prokka module can get after modules stuck if the header file longer 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 * fix bakta stats parsing * 81 add tool mob suite (#90) * 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 * update singularity config * fixed kofamscan download * fix dockerfile * Fix unicycler tag * use only docker images to avoid timeout error * use docker ocntainer to avoid singularity timeout * fixed resfinder for singularity * fixed docker image * fix gff2sql in singularity * use proper singularity images * fix singularity image download * fixed docker image * Add option for prebuilt db download (#94) * include module to download pre-built databases * update docs * 69 tools to use own docker image (#91) * 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 unicycler version (0.5.0--py310h6cc9453_3) * 96 error summary for bugfix release (#101) Update falmeida-py version * 98 include ices and prophage annotation in json summary (#106) * Try Dockerfile fix * Update Dockerfile * Update Dockerfile * Update CHANGELOG.md * 100 update pipeline docker images from docker tags to docker shasum (#108) * fix singularity run options * fix misc dockerfile * update renv docker image environment * update docker images to use shasum * Update CHANGELOG.md * 107 duplicate reads to unique read names (#109) * 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 changelog * Update docs for v3.3 (#110) * 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 citation information * add citation example * Update CHANGELOG.md * 111 error on summary step when missing annotationidtxt key (#112) * 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
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Relates to #80 to add a pre-formatted database in .tar.gz format for users.