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Release 2.3.0#137

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Daniel-VM merged 90 commits intomasternf-core/bacass:masterfrom devnf-core/bacass:devCopy head branch name to clipboardJun 12, 2024

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Commits on Nov 6, 2023

• add kmerfinder for shortreads

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• add module kmerfinder summary report

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Commits on Nov 14, 2023

• add module to find and download reference genome

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• fix kmerfinder summary input

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Commits on Nov 17, 2023

• update kmerfinder output file extension

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• add kmerfinder refseqid to meta

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• fix url in kmerfinder donwload ref

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• temporary commit

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Commits on Nov 19, 2023

• group assemblies by refseqid

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Commits on Nov 20, 2023

• allow global quast and by-refseqid quast

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Commits on Nov 21, 2023

• move kmerfinder processing to subworkflow plus output refactoring

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• Merge branch 'bu-isciii_tmp' into buisciii-develop

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• allow quast to standard and byrefseq data

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Commits on Nov 22, 2023

• add byrefseq quast reports to multiqc and patch quast

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Commits on Jan 2, 2024

• add byrefseq quast reports to multiqc and patch quast

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• update multiqc and append fastp metrics to assmebly metrics df

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• add new method to complie kmerfinder results into multiqc report

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• add long reads assembly metrics to custom multiqc

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• Merge branch 'buisciii-develop' of https://github.com/Daniel-VM/bacass into buisciii-develop

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Commits on Jan 3, 2024

• fix custom multiqc when kmerfinder is not invoked

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Commits on Jan 4, 2024

• add custom multiqc for hybrid assembly

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• add file-check-exist and rename variables

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Commits on Jan 5, 2024

• update documentation and add save_trimmed option

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• add fastp additional options and fix input sample path

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Commits on Jan 15, 2024

• allow module to emit tsv report

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Commits on Feb 22, 2024

• add kmerfinder for shortreads

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  b73e3f0

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• add module kmerfinder summary report

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  764a3d0

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• add module to find and download reference genome

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  0f07718

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• fix kmerfinder summary input

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  e072b2d

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• update kmerfinder output file extension

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  8baded1

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• add kmerfinder refseqid to meta

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  9bdc67e

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• fix url in kmerfinder donwload ref

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• temporary commit

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• group assemblies by refseqid

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  071d334

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• allow global quast and by-refseqid quast

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  7822c4b

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• move kmerfinder processing to subworkflow plus output refactoring

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• allow quast to standard and byrefseq data

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  6e7e0fa

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• add byrefseq quast reports to multiqc and patch quast

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  a184e41

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• update multiqc and append fastp metrics to assmebly metrics df

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  997fc91

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• add new method to complie kmerfinder results into multiqc report

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  07f6c39

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• add long reads assembly metrics to custom multiqc

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  e0481e0

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• fix custom multiqc when kmerfinder is not invoked

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  04ca4b3

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• add custom multiqc for hybrid assembly

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  3c6297a

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• add file-check-exist and rename variables

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  660799d

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• update documentation and add save_trimmed option

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  aeaa20e

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• add fastp additional options and fix input sample path

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  95d965d

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• allow module to emit tsv report

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  b33a37d

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• fix kmerFinder by narrowing down the reference genomes to a single winning candidate

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Commits on Mar 19, 2024

• Fix divergen branches when mergin remote origin/buisciii-develop into buisciii-develop

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Commits on Apr 16, 2024

• Fix: save_trimmed_fail is a boolean

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Commits on Apr 17, 2024

• bump version 2.3.0dev

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• add reviewer suggestions on #126

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• Merge pull request #126 from Daniel-VM/dev

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Commits on Apr 22, 2024

• Merge remote-tracking branch 'upstream/dev' into HEAD

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• update CHANGELOG #125

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• Merge pull request #125 from nf-core/fix_schema_boolean

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Commits on May 8, 2024

• Template update for nf-core/tools version 2.14.0

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Commits on May 9, 2024

• Template update for nf-core/tools version 2.14.1

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Commits on May 16, 2024

• update to nf-core-tools-2.14.1

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• update changelog #133

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Commits on May 17, 2024

• Merge pull request #133 from Daniel-VM/update_nf-core-tools-2.14.1

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• fix samples reported in prokka/bakta multiqc report

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• update changelog #134

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• add multiqc report generic method to name samples

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• Merge pull request #134 from Daniel-VM/dev

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• fix uncompress method to parse kmerfinder db

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• add new kmerfinderdb untar method and fix standalone py

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Commits on May 20, 2024

• fix step to prepare kmerfinderdb

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• add kmerfinder to pipeline tests

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• kmerfinder subworkflow cleaning

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• Merge branch 'buisciii-develop' into dev

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• remove unnecessary dependencies after merging branch

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• fix linting after mergin branch

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• update CHANGLEOG in #135

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Commits on May 23, 2024

• add reviewer suggestions #135 pt.1

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• fix multqc channels

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• add reviewer suggestions #135 pt.2

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• fix test_long_miniasm git CI test in #135

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Commits on May 24, 2024

• Merge pull request #135 from Daniel-VM/dev

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• bump version 2.3.0

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• Merge pull request #136 from Daniel-VM/dev

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Commits on May 25, 2024

• added reviewer suggestions before v2.3.0 release

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Commits on May 27, 2024

• Merge pull request #138 from Daniel-VM/dev

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Commits on May 30, 2024

• reviewer 2 suggestions before v2.3.0 release

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Commits on Jun 3, 2024

• add stable url

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• Merge pull request #139 from Daniel-VM/dev

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Commits on Jun 12, 2024

• added missing liscence

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• Merge pull request #140 from Daniel-VM/dev

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• Update date of release in CHANGELOG.md #137

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• Merge pull request #141 from Daniel-VM/dev

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