Code

Cnv for real now#513

Code

Merged

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

  FriederikeHanssen

  committed
  c894353

• nf-core update mpileup

  FriederikeHanssen

  committed
  3358c23

• first controlfreec version

  FriederikeHanssen

  committed
  98c0ddc

• install controlfreec again with significance script

  FriederikeHanssen

  committed
  2f51ecc

• add controlfreec plotting modules

  FriederikeHanssen

  committed
  5f070bf

Commits on Mar 26, 2022

• Install freec2circos

  FriederikeHanssen

  committed
  44a1a37

• Work on pari contronlfreec implementation to get tests to pass

  FriederikeHanssen

  committed
  c0473a9

Commits on Mar 28, 2022

• First running version of ControlFreec

  FriederikeHanssen

  committed
  ffe76cd

Commits on Mar 30, 2022

• nf-core modules update freec to fix typo

  FriederikeHanssen

  committed
  245c1d9

• fix manta-strelka combination output channel name

  FriederikeHanssen

  committed
  be78070

• add nextflow config with test args for freec

  FriederikeHanssen

  committed
  241ef86

• Fix StrelkaBP input mapping

  FriederikeHanssen

  committed
  577cff8

• Add StrelkaBP tests

  FriederikeHanssen

  committed
  a36a986

• Add controlfreec paired conf

  FriederikeHanssen

  committed
  20667a7

Commits on Mar 31, 2022

• Copy controlfreec map :crying:

  FriederikeHanssen

  committed
  0a33326

• same quotes, same spaces

  FriederikeHanssen

  committed
  afda89c

Commits on Apr 5, 2022

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

  FriederikeHanssen

  committed
  a7ce499

Commits on Apr 7, 2022

• Make controlfreec workflow agnostic to paired or single input

  FriederikeHanssen

  committed
  6ab729e

• add required cf input to tumor vc workflow

  FriederikeHanssen

  committed
  47e0497

• Adapt fodler structure to use controlfreec subworkflow

  FriederikeHanssen

  committed
  163c154

Commits on Apr 8, 2022

• nf-core modules update -all

  FriederikeHanssen

  committed
  6390a5d

• nf-core modules update -all

  FriederikeHanssen

  committed
  fa6de98

• prettier

  FriederikeHanssen

  committed
  817d718

• tests pass

  FriederikeHanssen

  committed
  50b1dda

Commits on Apr 11, 2022

• update samtools to 1.15.1

  FriederikeHanssen

  committed
  fffedb7

• Add CF testing

  FriederikeHanssen

  committed
  5c26303

• see if removing controlfreec tests fixes log not found error

  FriederikeHanssen

  committed
  f8681b2

• see if removing controlfreec tests fixes log not found error

  FriederikeHanssen

  committed
  6e8b5b9

• Merge branch 'dev' into cnv_for_real_now

  FriederikeHanssen

  authored
  a64dce0

Commits on Apr 12, 2022

• update manta

  FriederikeHanssen

  committed
  16372f8

Commits on Apr 13, 2022

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

  FriederikeHanssen

  committed
  71c317c

• Functional Tumoronly Cf workflow

  FriederikeHanssen

  committed
  c34c4fd

• add optional tar.gz for chromosome files

  FriederikeHanssen

  committed
  50f4137

• comment my decisions

  FriederikeHanssen

  committed
  2ba2458

• use test data from test data repo

  FriederikeHanssen

  committed
  79865e4

• Add untar module

  FriederikeHanssen

  committed
  1b8daca

• make the linters happy

  FriederikeHanssen

  committed
  c0187af

• Merge branch 'dev' into cnv_for_real_now

  FriederikeHanssen

  authored
  c07eb79

• add cf to CI test

  FriederikeHanssen

  committed
  a82f588

Commits on Apr 14, 2022

• Fix output paths

  FriederikeHanssen

  committed
  3351d2a

• Update conf/modules.config

  Show description for 97b0999
  

  FriederikeHanssen

  and

  maxulysse

  authored
  97b0999

• update schema

  FriederikeHanssen

  committed
  33d908f

• update schema

  FriederikeHanssen

  committed
  134c8de

• Fix intend

  FriederikeHanssen

  committed
  42dc81c

• remove empty workflow

  FriederikeHanssen

  committed
  88767f5

• prettier

  FriederikeHanssen

  committed
  1ac969f

• update modules

  FriederikeHanssen

  committed
  9d79d70