Pipeline update: v3.1.3 #61
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* 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
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