Tags: fmalmeida/bacannot
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Wrap-up patch release v3.3.1 (#113) * 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
Wrap-up v3.3 for release (#93) * 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
Latest updates from dev (#74) * update hmmer to working version with PGAP * update hmmer to working version with PGAP (#59) (#60) * Adding option for using `bakta` (#58) * first bakta addition test * Fixing error when phigaro output was empty (#55) (#56) * adding checkIfExists rules to input loading * Update build.sh * fixed report if else statement * updated version and changelog * fix example samplesheet url * Create nf-core-bacannot-compare_logo_dark.png * Update phigaro.nf * Update CHANGELOG.md * Update CHANGELOG.md * Update .gitignore * Update bacannot.nf * workflow runs from top to bottom * workflow correctly working * changing version manifest * explaining how to use bakta * adding variables to generic annotation * adding victors backup db * report_general understands bakta * report_resistance understands bakta * update hmmer to working version with PGAP * update hmmer to working version with PGAP (#59) * update hmmer to working version with PGAP (#59) (#60) * Update resfinder2gff.py * Update addBedtoolsIntersect.R * Update addBedtoolsIntersect.R * Update addBedtoolsIntersect.R * Update addBedtoolsIntersect.R * Update docker.config * download db if not available * Update merge_annotations.nf * Update merge_annotations.nf * update process label * Update merge_annotations.nf * fix docker file ownerships * added retry label for bakta * update changelog * changing to new version * add falmeida-py scripts to docker * Create generate_dockers.sh * Minor improvements for custom database annotation (#67) * Add step making Blast DB when annotating custom db Blast database throw error for no alias or index file found for nucleotide database, when using blastn. Thus, make blast database before execute blastn to custom database on genome. * Remove space when generate link in Shiny markdown Whitespace occurs when generated links for custom database report in Shiny markdown. Specify seperate string to emtpy string to fix this. * fix: script was calling an out of bounds value * handle exceptions and missing values * increment test profile * also build for proteins * Use correct version of customdb_gffs in REPORTS module Co-authored-by: fmalmeida <[email protected]> * fixed docker images * resfinder now uses conda env * rgi does not have --exclude_nudge anymore * add circos conf files * fix indentation * add circos sub-workflow calling * add circos tool * added karyotype and gc_skew modules * fix indentation * modules now have a channel suitable for summary generation * include summary generation module * update docker image * add aro index tsv * add amrfinder2tsv module * add bacannot json summary generation * update docker images * add new modules * added binaries for circos plot * update docker files * add label to module * finalise modules preparing data for circos * include whole circos 'pathway' in workflow * add circos module * circos plot currently functional * re-organised circos outputs * ameliorate default version of circos plot * fixed docker image * fixed custom annotation problem in server * added circos plot with easy_circos * circos plot properly being generated * update changelog * update readme * update documentation * fix tool name * fix dir * update indentation * fixed schema * add pipefail * fix docker image Co-authored-by: Cy <[email protected]>
75 upgrade bakta to 151+ (#76) * updating BAKTA docker image tag * make the version tags of additional non-core tools (bakta, flye and unicycler) a parameter that can be configured * update json schema with new parameters * update docs and version number * fix indentation * update bakta version to latest before release
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