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85 prokka module can get after modules stuck if the header file longer than 20 and not separated by tab or space #89

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merged 3 commits into from
Mar 3, 2023
Merged

85 prokka module can get after modules stuck if the header file longer than 20 and not separated by tab or space #89

merged 3 commits into from
Mar 3, 2023

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fmalmeida
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Add a small awk statement to clean big fasta headers only allowing 20 characters. Added to both prokka and bakta.
Should fix #85

@fmalmeida fmalmeida added the bug Something isn't working label Mar 3, 2023
@fmalmeida fmalmeida linked an issue Mar 3, 2023 that may be closed by this pull request
Prokka module can get after modules stuck if the header file longer than 20 and not separated by tab or space #85
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@fmalmeida fmalmeida added this to the v3.3 milestone Mar 3, 2023
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fmalmeida commented Mar 3, 2023 •
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Passed:

  • Prokka
  • Bakta

@fmalmeida fmalmeida merged commit 6fff59a into dev Mar 3, 2023
@fmalmeida fmalmeida deleted the 85-prokka-module-can-get-after-modules-stuck-if-the-header-file-longer-than-20-and-not-separated-by-tab-or-space branch March 3, 2023 11:39
@fmalmeida fmalmeida mentioned this pull request Mar 3, 2023
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fmalmeida added a commit that referenced this pull request Oct 1, 2023
@fmalmeida
Wrap-up v3.3 for release (#93)
46fcb59 
* 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
@fmalmeida
Wrap-up patch release v3.3.1 (#113)
9f1ed94 
* 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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Prokka module can get after modules stuck if the header file longer than 20 and not separated by tab or space
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@fmalmeida