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Methylation#543

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dennishendriksen wants to merge 60 commits intomainmolgenis/vip:mainfrom PoC/Methylationmolgenis/vip:PoC/MethylationCopy head branch name to clipboard

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Commits on Oct 26, 2023

• feat: accept base modification workflow and input

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Commits on Nov 1, 2023

• feat: add first draft vip base modification workflow

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• feat: added first draft base modification config file

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• fix: input only tsv file not pod5 dir

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Commits on Nov 13, 2023

• feat: added working dorado tool

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• feat: added config for dorado tool

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• fix: no process named samtools fixed

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• Merge branch 'main' into PoC/Methylation, use vip relase 7.0.0

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Commits on Nov 16, 2023

• Feat: added modules for pipeline

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• feat: updated workflow for modkit

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• feat: updated config for modkit

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Commits on Nov 21, 2023

• fix: updated modules and added template dorado tool

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• Update: newest vip version

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Commits on Nov 28, 2023

• docs: updated usage in README.md

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Commits on Nov 29, 2023

• fix: improved workflow and added comments

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• fix: improved dorado process and added comments

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• fix: improved process and added comments

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• fix: improved process samtools and added comments

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• fix: updated config mod file and added comments

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• fix: added label to samtools workflow

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Commits on Dec 11, 2023

• feat: change to reference genome build 38

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Commits on Dec 12, 2023

• feat: add tool methplotlib for methylation frequency per region

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• feat: add toolconfig for tool methplotlib

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Commits on Dec 13, 2023

• bug: methplotlib tool does not yet work

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• feat: add conversion bam to cram to continue with vip pipeline

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Commits on Dec 14, 2023

• fix: modified base pipeline until making of cram file

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• Merge branch 'main' into PoC/Methylation, update to newest version vip 7.1.0

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Commits on Dec 15, 2023

• Merge branch 'main' into PoC/Methylation, update to vip 7.2.0

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• fix: undefined parameter

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• fix: undefined parameter

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Commits on Dec 21, 2023

• Merge branch 'main' of https://github.com/molgenis/vip into PoC/Methylation, go to VIP release v7.2.1

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Commits on Dec 22, 2023

• fix: reference no longer defined null and cpg island detected with modkit

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• fixcpg island detected with modkit

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Commits on Jan 22, 2024

• Feat: add report to accept bedMethyl files

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• Feat: fix bed to bedmethyl bug, add h to m conversion

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• Refactor: delete unessecary code and update variables

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Commits on Jan 23, 2024

• Refactor: change workflow name from mod to pod5

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• refactor: change module mod directory to pod5

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• Refactor: delete old mod workflow files

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• Update docs

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• Fix: pod5 to cram workflow variables found

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• Feat: added first modkit "draft" def file

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• Fix: cargo not found

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Commits on Jan 24, 2024

• Refactor: other method for mdokit def file

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• Add extension to bed file

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Commits on Jan 25, 2024

• Refactor: commit added to modkit.def

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• Feat: use docker images for Dorado and Modkit

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Commits on Jan 27, 2024

• Feat: add docker images to pod5 workflow

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• Feat: add a pod5 workflow test

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• Fix: fix typo in template parameter

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Commits on Jan 29, 2024

• Feat: validate dorado model parameter

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• Add modkit and dorado image to install.sh

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• Refactor: cleanup code and add test to docs

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• Fix: download Dorado correctly

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• Feat: Add dorado Fast, HAC and SUP models to resources

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Commits on Jan 30, 2024

• Update requirements.md

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• Add: add installation of tool to README.md

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• Update docs lead to merge branch 'PoC/Methylation' of https://github.com/molgenis/vip into PoC/Methylation

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• README.md: need to load awscli to execute pod5 test

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• README.md: add path to output test pod5

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