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Release 2.2.0#122

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Daniel-VM merged 76 commits intomasternf-core/bacass:masterfrom devnf-core/bacass:devCopy head branch name to clipboardApr 4, 2024

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Commits on Oct 23, 2023

• bump version to 2.2.0dev

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Commits on Oct 24, 2023

• fix indentation in mainfest

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• update formatting in comments of allowed options

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• Merge pull request #100 from Daniel-VM/bump-version-2.2.0dev

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Commits on Oct 26, 2023

• update bakta to v1.8.2

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• Merge pull request #103 from Daniel-VM/dev

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Commits on Oct 27, 2023

• add nfcore module dragonfyle

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• create test for assembly with dragonflye

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• tmp fix for handling gzip/no-gzip assemblies

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• add genome_size value in the input file to meta map

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• add genome_size value to ext.args in dragonflye

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• add dragonfly documentation plus fixme message in workflow

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• fix prettier

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Commits on Oct 28, 2023

• fix processing of gziped assemblies for gene annotation

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Commits on Oct 30, 2023

• fix ext.args and update help text on dragonflye module

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• Merge branch 'module_dragonflye' into dev

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• update changelog #104

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Commits on Oct 31, 2023

• fix condition to parse gsize in dragonflye module conf

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• patch dragonflye module to allow short-reads polishing of draft genome

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Commits on Nov 2, 2023

• applied reviewer suggestions #104

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• Merge pull request #104 from Daniel-VM/dev

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• porechop patch to prevent input file from being overwritten with output file

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Commits on Nov 3, 2023

• update dragonflye version and fix output file name

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• add dragonflye hybrid-mode to readme

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• Merge branch 'dragonflye_hybridmode' into dev

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• temp fix of dragonflye modules.config

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Commits on Nov 6, 2023

• complete fix of dragonflye module config

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Commits on Nov 7, 2023

• update CHANGELOG #106

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Commits on Nov 9, 2023

• add reviewer suggestions #106

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• fix prettier #106

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• add profile test_hybrid_dragonflye to github CI test

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• Merge pull request #106 from Daniel-VM/dev

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Commits on Dec 19, 2023

• Template update for nf-core/tools version 2.11

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Commits on Dec 20, 2023

• Template update for nf-core/tools version 2.11.1

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Commits on Jan 29, 2024

• Template update for nf-core/tools version 2.12

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Commits on Feb 12, 2024

• merge nf-core template v2.12

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• fix input file format after template update

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• fix linting module update required

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Commits on Feb 13, 2024

• fix linging after template v2.12 update

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• update changelog in PR #111

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• fixed git CLI test by recovering patched module #111

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• fix prettier #111

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Commits on Feb 19, 2024

• add reviewer suggestions in #111

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• Merge pull request #111 from Daniel-VM/dev

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Commits on Feb 20, 2024

• Template update for nf-core/tools version 2.13

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Commits on Feb 29, 2024

• Template update for nf-core/tools version 2.13.1

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Commits on Mar 18, 2024

• Merge branch 'nf-core-template-merge-2.13.1' into dev

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• fix input parsing after template update

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• remove conflicting null val injected via ifempty

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Commits on Mar 19, 2024

• workaround to fix test profile long regarding null channel ch_versions

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• fix linting after updating to template 2.13.1

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• fix old quote format in docs

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• fix prettier and update changelog #117

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• fix linting x2 #117

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• applying reviewer suggestions on #117

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• Merge pull request #117 from Daniel-VM/dev

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Commits on Mar 21, 2024

• replace image repo

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• fix lint warning regarding version channel

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• updated local modules-subworkflows

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• update all nf-core modules

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• update changelog #120

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• recover dfast version from the updated one with broken dependencies

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• fix miniap2 input channels after updating modules

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• update local modules structure

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• fix fastp linting #120

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Commits on Mar 22, 2024

• Merge pull request #120 from Daniel-VM/dev

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Commits on Mar 27, 2024

• bump version 2.2.0

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Commits on Mar 30, 2024

• Merge pull request #121 from Daniel-VM/dev

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• fix download pipeline workflow - gitCLI

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• fix linting error after updating workflow download pipeline

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• update changelog #123

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Commits on Apr 2, 2024

• Merge pull request #123 from Daniel-VM/dev

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Commits on Apr 3, 2024

• add reviewer suggestions in PR #122

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• add reviewer 2 suggestions in PR #122

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Commits on Apr 4, 2024

• Update .github/CONTRIBUTING.md in #124

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• Merge pull request #124 from Daniel-VM/dev

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