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@leepc12 leepc12 released this 13 Jan 16:51
· 394 commits to master since this release
v1.3.5.1
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Learn about vigilant mode.

Conda users need to re-install pipeline's Conda env.

$ bash scripts/uninstall_conda_env.sh
$ bash scripts/install_conda_env.sh

Output file name change

  • Pooled TAG-ALIGN file will have a fixed prefix of rep.pooled instead of using rep1's prefix.

Change in default parameters

  • chip.filter_picard_java_heap: 4G to dynamic (chip.filter_mem_mb)
  • chip.gc_bias_picard_java_heap: 6G to 10G

Troubleshooting for failed pipelines

  • Added some help texts for stringent IDR threshold

Added important GNU apps to Conda env

  • tar: to sort by filename tar --sort
  • grep: to use Perl style regular expression grep -P

Misc.

  • Downgraded Java version 11 -> 8 in docker/singularity images.
  • Output def JSON file for Croo: v3 released.
  • bowtie2 log is directly printed to STDOUT instead of printing to .align.log
  • removed wrong arrow (FASTQ R2 -> chip.xcor) in task graph in Croo's HTML report.
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