Code

updating GATK#1419

Code

Merged

maxulysse merged 33 commits intonf-core:devnf-core/sarek:devfrom asp8200:update_gatkasp8200/sarek:update_gatkCopy head branch name to clipboardFeb 23, 2024

+1,532-109

Commits

Commits on Feb 22, 2024

• updating gatk/haplotypecaller

  asp8200

  committed
  5cdc724

  Copy full SHA for 5cdc724

• Temporarily disabling nf-test for gatk/haplotypecaller

  asp8200

  committed
  9694d25

  Copy full SHA for 9694d25

• Temporarily disabling nf-test for gatk4/haplotypecaller

  asp8200

  committed
  1ec78f1

  Copy full SHA for 1ec78f1

• updating gatk4/applybqsr and gatk4/applyvqsr

  asp8200

  committed
  d320370

  Copy full SHA for d320370

• Removing redundant input-channel dbsnp_vqsr from BAM_VARIANT_CALLING_HAPLOTYPECALLER

  asp8200

  committed
  b995340

  Copy full SHA for b995340

• updating gatk4/baserecalibrator

  asp8200

  committed
  fd62f6d

  Copy full SHA for fd62f6d

• Temporarily disabling nf-test for gatk4/baserecalibrator

  asp8200

  committed
  757f921

  Copy full SHA for 757f921

• updating gatk4/calculatecontamination

  asp8200

  committed
  8b2dbc2

  Copy full SHA for 8b2dbc2

• updating gatk4/cnnscorevariants

  asp8200

  committed
  be434c7

  Copy full SHA for be434c7

• updating gatk4/createsequencedictionary

  asp8200

  committed
  3efde7e

  Copy full SHA for 3efde7e

• updating gatk4/estimatelibrarycomplexity

  asp8200

  committed
  c12c40a

  Copy full SHA for c12c40a

• updating gatk4/filtermutectcalls

  asp8200

  committed
  2b47d51

  Copy full SHA for 2b47d51

• updating gatk4/filtervarianttranches

  asp8200

  committed
  bec8c99

  Copy full SHA for bec8c99

• updating gatk4/gatherbqsrreports

  asp8200

  committed
  50ad22c

  Copy full SHA for 50ad22c

• updating gatk4/gatherpileupsummaries

  asp8200

  committed
  b8c1902

  Copy full SHA for b8c1902

• updating gatk4/genomicsdbimport

  asp8200

  committed
  dbcfb21

  Copy full SHA for dbcfb21

• Temporarily disabling nf-test for gatk4/genomicsdbimport

  asp8200

  committed
  057ef59

  Copy full SHA for 057ef59

• updating md5sum for mutect2.filtered.vcf.gz.filteringStats.tsv

  asp8200

  committed
  1cf073a

  Copy full SHA for 1cf073a

• updating gatk4/genotypegvcfs

  asp8200

  committed
  d66027a

  Copy full SHA for d66027a

• updating gatk4/getpileupsummaries

  asp8200

  committed
  ee2f427

  Copy full SHA for ee2f427

• updating gatk4/intervallisttobed

  asp8200

  committed
  2c15196

  Copy full SHA for 2c15196

• updating gatk4/learnreadorientationmodel

  asp8200

  committed
  3ffb94c

  Copy full SHA for 3ffb94c

• updating gatk4/markduplicates

  asp8200

  committed
  bd500cd

  Copy full SHA for bd500cd

• Temporarily disabling nf-test for gatk4/markduplicates

  asp8200

  committed
  c0312f7

  Copy full SHA for c0312f7

• updating gatk4/mergemutectstats

  asp8200

  committed
  f3fe6df

  Copy full SHA for f3fe6df

• updating gatk4/mergevcfs

  asp8200

  committed
  7cc1609

  Copy full SHA for 7cc1609

• Temporarily disabling nf-test for gatk4/mergevcfs

  asp8200

  committed
  dd135e9

  Copy full SHA for dd135e9

• updating gatk4/mutect2

  asp8200

  committed
  b548bff

  Copy full SHA for b548bff

• updating gatk4/variantrecalibrator

  asp8200

  committed
  1095957

  Copy full SHA for 1095957

• Updating changelog

  asp8200

  committed
  f998adb

  Copy full SHA for f998adb

• Updating changelog

  asp8200

  committed
  ac598b8

  Copy full SHA for ac598b8

Commits on Feb 23, 2024

• Adding meta in certain input-channels in call to BAM_VARIANT_CALLING_HAPLOTYPECALLER

  asp8200

  committed
  9bb7bb4

  Copy full SHA for 9bb7bb4

• Removing meta in certain input-channels in call to GATK4_HAPLOTYPECALLER

  asp8200

  committed
  9ab72f2

  Copy full SHA for 9ab72f2