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@jluebeck jluebeck released this 23 Mar 01:27
· 28 commits to master since this release
v1.3.1
b76c005
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Learn about vigilant mode.
  • Remove bloat from container images (Docker 8.7GB -> 2.2GB. Singularity 6.0GB -> 636MB)
    • This was due to unnecessary, massive pytorch GPU packages being included with CNVkit's dependencies by default.
  • Remove bloat from standalone installer script (pytorch GPU packages)
  • Add bedtools as a dependency
  • GroupedAnalysisAmpSuite.py will automatically compute feature similarity scores.
  • GroupedAnalysisAmpSuite.py bugfix when CNV seeds are already provided in input table.
  • GroupedAnalysisAmpSuite.py detect improperly formatted input table.
  • Automatically detect samtools version (removes --use_old_samtools)
  • Warn user if alt contigs in bam header.
  • Fix logging of AA version in run_metadata.json.
  • Better protection for bad inputs (e.g. user gave same fastq twice, bam file with spaces in name)
  • Fix no amp samples not getting ref genome version in run_metadata.json
  • Update Rscript package installation in containers.
  • Bugfix to manual specification of Singularity image file location
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