Code

Refactor Variant Calling#497

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FriederikeHanssen merged 54 commits intonf-core:devnf-core/sarek:devfrom FriederikeHanssen:cnvFriederikeHanssen/sarek:cnvCopy head branch name to clipboardMar 24, 2022

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Commits

Commits on Mar 11, 2022

• Install controlfreec

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Commits on Mar 15, 2022

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

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• install ascat

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Commits on Mar 19, 2022

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

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• Pull deepvariant into own sw

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Commits on Mar 21, 2022

• Pull all germline VC steps into own subworkflows

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• Fix broken imports

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• Add slightly ugly if's to subworkflows to avoid printing of unrun processes to terminal. Sorry @maxulysse :( we'll keep improving this

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• fix output variable names

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• more refactoring

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Commits on Mar 22, 2022

• Fix import path

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• Comment, typos and beautify deepvariant sw

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• Comment, typos and beautify manta_germline sw

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• Comment, typos and beautify strelka sw

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• Rename from RUN_TOOL to TOOL

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• Rename MANTA to MANTA_GERMLINE

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• Start including mutect with new when syntax

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• rename subworkflows when accessing output

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• Rename Strelka sw to STRELKA_SINGLE

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• Name back to RUN_TOOL, subworkflows and modules can't have the same name, subworkflow will take priority over included module

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• Remove groupTuple, do branching based on num_intervals, since meta maps have different id fields when intervals are present

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• Rework manta and strelka_somatic subworkflow

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• Reorder to follow same structure everywhere

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• Add missing versions

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• indent comments

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• Formatting

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• Formatting

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• More Formatting & comments

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• Sort input correctly helps a lot, also fix typos

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• Use nf-core/manta

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• Add in a bunch of tests for mainly tumor / somatic tools

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• Add in a bunch of tests for mainly tumor / somatic tools

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• Revert test ressource

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• add freebayes tests

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• update sample names to make sure the tests are not overwritting each other

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• update sample names to make sure the tests are not overwritting each other

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• Fix manta tests

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• refactor mutect2 tumor_only with new syntax

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• Add in mutect confs

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• update strelka output paths

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Commits on Mar 23, 2022

• remove tbi from sw outputs as not needed for annotation

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• Fix run_freebayes input channels

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• Reorganize vc subworkflow after code review

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• add mutect2 test

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• tests pass locally, whats wrong with this

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• Add tumor only mutects + tests, cause thats important too

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• Add in mutect2 somatic

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• Add msisensorpro tests and fix bed file for it

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• linting

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• Set back ressource values for tests

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• Always publish ceepvariant gvcf they are generated anyways

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• Correct strelka and msisensorpro output paths

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Commits on Mar 24, 2022

• Fix num_intervals when no_intervals

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• indent from review & add meta clone in the hopes it fixes Concurrentmodification

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