Code

Cnv for real now#513

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FriederikeHanssen merged 47 commits intonf-core:devnf-core/sarek:devfrom FriederikeHanssen:cnv_for_real_nowFriederikeHanssen/sarek:cnv_for_real_nowCopy head branch name to clipboardApr 14, 2022

+1,593-389

Commits

Commits on Mar 25, 2022

• Add in controlfreec sw

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  c894353

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• nf-core update mpileup

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  3358c23

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• first controlfreec version

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• install controlfreec again with significance script

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• add controlfreec plotting modules

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Commits on Mar 26, 2022

• Install freec2circos

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• Work on pari contronlfreec implementation to get tests to pass

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Commits on Mar 28, 2022

• First running version of ControlFreec

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Commits on Mar 30, 2022

• nf-core modules update freec to fix typo

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• fix manta-strelka combination output channel name

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• add nextflow config with test args for freec

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• Fix StrelkaBP input mapping

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• Add StrelkaBP tests

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• Add controlfreec paired conf

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Commits on Mar 31, 2022

• Copy controlfreec map :crying:

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• same quotes, same spaces

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Commits on Apr 5, 2022

• Add tumor only controlfreec (can't test, as test data won't pass)

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Commits on Apr 7, 2022

• Make controlfreec workflow agnostic to paired or single input

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• add required cf input to tumor vc workflow

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• Adapt fodler structure to use controlfreec subworkflow

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Commits on Apr 8, 2022

• nf-core modules update -all

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• nf-core modules update -all

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• prettier

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• tests pass

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Commits on Apr 11, 2022

• update samtools to 1.15.1

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• Add CF testing

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  5c26303

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• see if removing controlfreec tests fixes log not found error

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  f8681b2

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• see if removing controlfreec tests fixes log not found error

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  6e8b5b9

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• Merge branch 'dev' into cnv_for_real_now

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Commits on Apr 12, 2022

• update manta

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Commits on Apr 13, 2022

• Finish up somatic CF, works locally tests won't pass because of local folder

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• Functional Tumoronly Cf workflow

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• add optional tar.gz for chromosome files

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• comment my decisions

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• use test data from test data repo

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• Add untar module

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• make the linters happy

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• Merge branch 'dev' into cnv_for_real_now

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• add cf to CI test

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Commits on Apr 14, 2022

• Fix output paths

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• Update conf/modules.config

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• update schema

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• update schema

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• Fix intend

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  42dc81c

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• remove empty workflow

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• prettier

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• update modules

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