Code

Support for PureCN#1710

Code

Draft

lbeltrame wants to merge 19 commits intonf-core:devnf-core/sarek:devfrom DIncalciLab:purecn-supportDIncalciLab/sarek:purecn-supportCopy head branch name to clipboard

+1,940-2

Commits

Commits on Oct 29, 2024

• Add PureCN modules to be used afterwards (easy part)

  lbeltrame

  committed
  1a2442b

  Copy full SHA for 1a2442b

• Add more required modules

  lbeltrame

  committed
  0ad7279

  Copy full SHA for 0ad7279

• Totally untested skeleton of the workflow

  lbeltrame

  committed
  774e86c

  Copy full SHA for 774e86c

• Provide both the intervals from PureCN and BED

  lbeltrame

  committed
  853cb4b

  Copy full SHA for 853cb4b

• Patch intervalfile not to use the genome argument

  lbeltrame

  committed
  12fc01c

  Copy full SHA for 12fc01c

• Patch out genome also from purecn/run

  lbeltrame

  committed
  59c1545

  Copy full SHA for 59c1545

• Remove genome from the subworkflow, too

  lbeltrame

  committed
  25b55df

  Copy full SHA for 25b55df

• Finish hooking up the pipeline and fix linting

  lbeltrame

  committed
  fc426df

  Copy full SHA for fc426df

• Hook up parameters to the configuration

  lbeltrame

  committed
  d456dc2

  Copy full SHA for d456dc2

• Merge remote-tracking branch 'origin/dev' into purecn-support

  lbeltrame

  committed
  dfc783e

  Copy full SHA for dfc783e

• Add recommended PureCN option

  lbeltrame

  committed
  bafa0b0

  Copy full SHA for bafa0b0

• Add also the min MAPQ quality for MuTect

  lbeltrame

  committed
  7b6eea7

  Copy full SHA for 7b6eea7

• Remove spurious include

  lbeltrame

  committed
  9921741

  Copy full SHA for 9921741

• Remove unneeded include

  lbeltrame

  committed
  74929cb

  Copy full SHA for 74929cb

Commits on Oct 30, 2024

• Fix linting (hopefully) by doing patches

  lbeltrame

  committed
  d956a4c

  Copy full SHA for d956a4c

• A little change to the PureCN module

  Show description for 6b666fe
  lbeltrame

  committed
  6b666fe

  Copy full SHA for 6b666fe

• Update patch

  lbeltrame

  committed
  5531eca

  Copy full SHA for 5531eca

• Require a MuTect2 VCF for PureCN

  Show description for 9e713bb
  lbeltrame

  committed
  9e713bb

  Copy full SHA for 9e713bb

• Enable PureCN with tumor-only Mutect too

  Show description for 82d477e
  lbeltrame

  committed
  82d477e

  Copy full SHA for 82d477e