v1.2.0

utils/resumer/resumer.py has been depcreated. Also, all tutorials and old documentation are abandoned. Please use Caper to run our pipeline. To organize outputs from metadata.json (output of Cromwell), use Croo

$ pip3 install caper croo

• Bug fixes

  • Remove intermediate files gradually as macs2 task progresses
  • Increase default disk size for Google Cloud for some heavy tasks (macs2, spp, bwa, filter, fingerprint)
  • new conda (conda activate instead of source activate)

• Others

  • Upgrade cromwell.jar from 34 to 38
  • split macs2 task into macs2 and macs2_signal_track
    • change in output name for signal track
      • macs2.sig_pval -> macs2_signal_track.pval_bw
      • macs2.sig_fc -> macs2_signal_track.fc_bw
    • task level test for two tasks
  • 3-dim fastqs array is not supported anymore
  • exclusion range for cross-correlation analysis
    • adding -x=min:max to run_spp.R in xcor
    • this will prevent xcor estimates wrong (negative) fragment len
  • fix KentUtils version at v369 in docker/singularity containers
  • added new example for Caper