Code

Fully implement annotation#35

Code

Merged

nvnieuwk merged 41 commits intodevnf-cmgg/structural:devfrom update-annotationnf-cmgg/structural:update-annotationCopy head branch name to clipboardMay 25, 2023

+1,695-355

Commits

Commits on Oct 7, 2022

• Template update for nf-core/tools version 2.6

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Commits on Jan 26, 2023

• Template update for nf-core/tools version 2.7.2

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Commits on Apr 14, 2023

• first steps

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  bacea54

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Commits on Apr 17, 2023

• fully implement the annotation

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• update test

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• offer a lamb to the linting gods

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• bug fix

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• offer a virgin to the linting gods (hope this is enough)

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Commits on Apr 19, 2023

• Add dynamic VCFanno config creation

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• go on a pilgrimage to the mountain of the linting gods and make a blood sacrifice

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  c6ca962

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• fix and update annotate test to stub

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• update vep container on stub runs

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• add postannotations support to the configs

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  f2d632f

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• simplified the vcfanno config code and made it smarter

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  37aafe9

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• added new fields from the annotsv vcf to the default configs

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• added a param for the default annotsv file name

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• fix small bug with param

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  b3d3a2c

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• fix small bug with param

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  1a67261

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• Add all default configs

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• sacrificing my firstborn child to the linting gods

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• Moved the unused configs to a separate folder

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Commits on Apr 20, 2023

• update configs

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  6c5f4e1

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• update vep config

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• add option to annotate on small variants with AnnotSV (real test files should still be added)

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  47a12fc

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• Remove unused VEP parameters

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  732dc8b

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• fix issues

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  10b11f7

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• add tests for small variants vcfs

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  799e4f9

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Commits on Apr 21, 2023

• add an option to also output the annotsv outputs

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Commits on May 8, 2023

• Merge wrongly placed commits (#40)

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Commits on May 11, 2023

• Template update for nf-core/tools version 2.8

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• Merge branch 'TEMPLATE' into template-v2.8

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• black linting

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• update modules

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• update modules

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  a0bde4d

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• fix local modules

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• bump

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• eclint

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• Merge pull request #42 from CenterForMedicalGeneticsGhent/template-v2.8

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Commits on May 25, 2023

• update genome in docs

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• update vcfanno configs retina and rpe

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• fix rpe bed file in config

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