Code

fix: fix somatic snappy (#477)#491

Code

Merged

ericblanc20 merged 29 commits intomainbihealth/snappy-pipeline:mainfrom 477-fix-somatic-snappybihealth/snappy-pipeline:477-fix-somatic-snappyCopy head branch name to clipboardMar 20, 2024

+1,392-311

Commits

Commits on Feb 1, 2024

• fix: snakemake silently requires numpy, pandas & cffi (issue #477)

  ericblanc20

  committed
  442a92e

• fix: remove the job dispache to critical, used medium (default queue) instead

  ericblanc20

  committed
  de49a4e

• fix: current (2024-02-01) sequenza incompatible with recent iotools R package

  ericblanc20

  committed
  a8a7eed

• fix: increase resource usage for PureCN

  ericblanc20

  committed
  40eec67

• feat: allow cbioportal export to use the most recent variant filtration using filter_list

  ericblanc20

  committed
  fb112bd

• fix: fix bug in adapter trimmin of unpaired samples

  ericblanc20

  committed
  2da149d

• test: sync the PureCN resources with test

  ericblanc20

  committed
  717d3d0

Commits on Feb 2, 2024

• fix: fix bug in old filtration method (using filter_sets)

  ericblanc20

  committed
  3e55ab5

Commits on Feb 12, 2024

• allow longer time for EB filter

  

  Manuela Benary

  committed
  25ed5e0

Commits on Feb 15, 2024

• fix: naming of path to baits reconciled between workflow & wrapper

  ericblanc20

  committed
  0c2b7c2

• docs: clarified filters usage in cbioportal_export

  ericblanc20

  committed
  019a2c1

• feat: add junctions table to STAR output

  ericblanc20

  committed
  2b5224f

• Merge branch '477-fix-somatic-snappy' of github.com:bihealth/snappy-pipeline into 477-fix-somatic-snappy

  ericblanc20

  committed
  05f0559

• test: fix eb_filter time resource

  ericblanc20

  committed
  dfa1c02

• feat: Add tumor mutational burden after filtration

  ericblanc20

  committed
  f9cd81c

Commits on Feb 23, 2024

• fix: indexing & overlaps between files with variants considered for EBFilter and those which aren't, and removed parallelization of EBFilter

  ericblanc20

  committed
  9472f31

• feat: add protection filter to the filtration step (whitelist some locii)

  ericblanc20

  committed
  8d28ff8

• feat: add purecn & sequenza to the choice of CNV callers for cBioPortal

  ericblanc20

  committed
  5e242d0

Commits on Feb 28, 2024

• docs: First draft of the somatic pipeline overview

  ericblanc20

  committed
  d5c4022

Commits on Mar 1, 2024

• fix: recent iotools package incompatible with latest sequenza

  ericblanc20

  committed
  42e2155

• feat: Add conda info & list to logs

  ericblanc20

  committed
  3242fed

• feat: add logs of individual coverage files generation to the set of cvnkit logs

  ericblanc20

  committed
  4034a4f

• docs: Improve documentation of selected steps

  ericblanc20

  committed
  1054cb2

• fix: re-enable logs for parallel jobs triggered by the ParallelMutect2BaseWrapper

  ericblanc20

  committed
  12b4513

• feat: collect logs and merge logs of individual filters, and improve step documentation

  ericblanc20

  committed
  67d798b

Commits on Mar 11, 2024

• docs: updated & improves somatic pipeline documentation

  ericblanc20

  committed
  fbc06f3

Commits on Mar 14, 2024

• style: make linting happy

  ericblanc20

  committed
  fc10dc2

• test: synchronize tests with the new logs

  ericblanc20

  committed
  55c49d1

Commits on Mar 20, 2024

• docs: fixed bunch of typos

  ericblanc20

  committed
  ed3a744