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grenepipe v0.11.0
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@lczech lczech released this 30 Nov 07:00
· 143 commits to master since this release
v0.11.0
c6b9333

Getting closer to v1.0.0! For now, this and the next couple of releases will still have some changes in the config.yaml that are not backwards compatible though, but hoping to make it future proof in the long run that way.

Notable Changes

  • De-indent reference genome and known variants in config
  • Switch to our improved version of HAF-pipe (petrov-lab/HAFpipe-line#9)
  • Add HAF-pipe per-sample concatenated tables
  • Add flag to turn off bcftools stats for avoiding variant calling to get MultiQC report
  • Add target for per-sample merged bam output
  • Add bcftools filter tool for VCF filtering
  • Add dbsnp option to all GATK tools, rename GATK config params
  • Add interleaved fastq test to generate table script for more robustness

Bug Fixes

  • Fix samtools tmp dir creation issues throughout the pipeline
  • Fix typo vqrs instead of vqsr
  • Fix GATK helper function location
  • Fix vep plugin download issue
  • Fix mapdamage conda env
  • Fix vcf index file duplication
  • Fix missing R package for MapDamage
  • Add flag files to avoid incomplete job executions
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