* 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

* 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 <felipemarques89@gmail.com>

…evelop