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0.4.2 Bug fixes
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@verku verku released this 05 Sep 12:01
· 199 commits to main since this release
0.4.2
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Updates related to large genome sizes and/or large sample sizes:

  • Run snpEff with option to specify -Xmx for large genomes and add the rules to cluster.yaml
  • Fix y-axis labels for mutational load plot so that there is no overlap for large sample sizes
  • Create new Docker images with bedtools and htslib (bgzip) so that VCF files filtered with bedtools can be compressed in a pipe to reduce intermediate file sizes

Minor bug fixes:

  • Update conda in GitHub actions to reduce run time
  • Shorten run time and lower number of cores for mutational load calculations in cluster.yaml
  • Remove temp flag from bam index file of rescaled bam files
  • Embed pipeline logo into GenErode pipeline report via link to file on repository so that the pipeline report can be moved to a different location
  • Fix "rerun incomplete" warning for rule make_reference_bed by separating it from the group job reference_prep_group

see https://github.com/NBISweden/GenErode/wiki/9.-Changelog#2022-09-05-version-042

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