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Adding option for using bakta #58

Merged
merged 34 commits into from
Sep 9, 2022
Merged

Adding option for using bakta #58

merged 34 commits into from
Sep 9, 2022

Commits on Nov 19, 2021

  1. first bakta addition test

    @fmalmeida
    fmalmeida committed Nov 19, 2021
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Commits on Jun 29, 2022

  1. 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
    @fmalmeida
    fmalmeida authored Jun 29, 2022
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Commits on Jul 4, 2022

  1. Merge branch 'master' into bakta

    @fmalmeida
    fmalmeida committed Jul 4, 2022
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  2. Update .gitignore

    @fmalmeida
    fmalmeida committed Jul 4, 2022
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  3. Update bacannot.nf

    @fmalmeida
    fmalmeida committed Jul 4, 2022
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Commits on Jul 5, 2022

  1. workflow runs from top to bottom

    @fmalmeida
    fmalmeida committed Jul 5, 2022
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Commits on Jul 6, 2022

  1. workflow correctly working

    @fmalmeida
    fmalmeida committed Jul 6, 2022
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Commits on Jul 23, 2022

  1. changing version manifest

    @fmalmeida
    fmalmeida committed Jul 23, 2022
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  2. explaining how to use bakta

    @fmalmeida
    fmalmeida committed Jul 23, 2022
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  3. adding variables to generic annotation

    @fmalmeida
    fmalmeida committed Jul 23, 2022
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  4. adding victors backup db

    @fmalmeida
    fmalmeida committed Jul 23, 2022
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  5. Merge branch 'master' into bakta

    @fmalmeida
    fmalmeida committed Jul 23, 2022
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  6. report_general understands bakta

    @fmalmeida
    fmalmeida committed Jul 23, 2022
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  7. report_resistance understands bakta

    @fmalmeida
    fmalmeida committed Jul 23, 2022
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Commits on Aug 29, 2022

  1. update hmmer to working version with PGAP

    @fmalmeida
    fmalmeida committed Aug 29, 2022
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Commits on Aug 30, 2022

  1. update hmmer to working version with PGAP (#59)

    @fmalmeida
    fmalmeida authored Aug 30, 2022
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Commits on Sep 2, 2022

  1. update hmmer to working version with PGAP (#59) (#60)

    @fmalmeida
    fmalmeida authored Sep 2, 2022
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Commits on Sep 3, 2022

  1. Update resfinder2gff.py

    @fmalmeida
    fmalmeida authored Sep 3, 2022
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  2. Update addBedtoolsIntersect.R

    @fmalmeida
    fmalmeida authored Sep 3, 2022
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  3. Update addBedtoolsIntersect.R

    @fmalmeida
    fmalmeida authored Sep 3, 2022
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  4. Update addBedtoolsIntersect.R

    @fmalmeida
    fmalmeida authored Sep 3, 2022
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  5. Merge branch 'master' into develop

    @fmalmeida
    fmalmeida committed Sep 3, 2022
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  6. Merge branch 'master' into bakta

    @fmalmeida
    fmalmeida committed Sep 3, 2022
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  7. Merge branch 'develop' into bakta

    @fmalmeida
    fmalmeida committed Sep 3, 2022
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  8. Update addBedtoolsIntersect.R

    @fmalmeida
    fmalmeida authored Sep 3, 2022
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  9. Merge branch 'master' into bakta

    @fmalmeida
    fmalmeida committed Sep 3, 2022
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  10. Update docker.config

    @fmalmeida
    fmalmeida committed Sep 3, 2022
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  11. download db if not available

    @fmalmeida
    fmalmeida committed Sep 3, 2022
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  12. Update merge_annotations.nf

    @fmalmeida
    fmalmeida authored Sep 3, 2022
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  13. Update merge_annotations.nf

    @fmalmeida
    fmalmeida authored Sep 3, 2022
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Commits on Sep 4, 2022

  1. update process label

    @fmalmeida
    fmalmeida authored Sep 4, 2022
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  2. Update merge_annotations.nf

    @fmalmeida
    fmalmeida authored Sep 4, 2022
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  3. fix docker file ownerships

    @fmalmeida
    fmalmeida committed Sep 4, 2022
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Commits on Sep 8, 2022

  1. added retry label for bakta

    @fmalmeida
    fmalmeida committed Sep 8, 2022
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