stjude/XenoCP

Issues

• Limit the memory usage of Xenocp

  #44 opened a year ago by zhaowsong
  5

• Job keeps failing

  #52 opened 9 months ago by bounlu
  0

• No space left on device

  #48 opened a year ago by zhaowsong
  6

• Add Singularity support

  #51 opened a year ago by mcrusch
  1

• Tie BAM is too large

  #45 opened a year ago by mcrusch
  1

• Update sample_data to reflect merged tie bams and contam lists

  #43 opened a year ago by mcrusch
  0

• Update build to work with gradle >= 7

  #46 opened a year ago by mcrusch
  1

• Clean BAM is larger than raw BAM files

  #42 opened a year ago by zhaowsong
  5

• input yaml file

  #41 opened a year ago by zhaowsong
  0

• Run command with Singularity will miss python packages.

  #39 opened a year ago by Autumn-Roy
  7

• Merge contam list and tie bams

  #4 opened 3 years ago by mcrusch
  0

• wdl/tools: XenoCP 3.1.4 tasks use 3.1.0 container image

  #28 opened 3 years ago by zaeleus
  1

• `MC` record data field not removed from unmapped records in final merged BAM

  #25 opened 3 years ago by zaeleus
  4

• Remove CIGAR strings for unmapped reads.

  #26 opened 3 years ago by claymcleod
  1

• Bug: unmapped read pairs are not preserved in output

  #9 opened 4 years ago by mcrusch
  2

• running xenocp with singularity

  #12 opened 4 years ago by xinyuwen
  10

• Singularity build of XenoCP

  #15 opened 4 years ago by adthrasher
  0

• Identification of mouse reads

  #14 opened 4 years ago by RaphaelHablesreiter
  8

• Error: Could not find or load main class org.stjude.compbio.sam.TweakSam

  #11 opened 5 years ago by lentaing
  3

• Does this need a default?

  #1 opened 5 years ago by adthrasher
  4