Release v1.2.0

[bryce-turner]

Major changes (Changes that cause restarts are in bold):

• All containers have been updated to use a more optimimally sized image, or using the image provided by the authors

  • We changed base containers over to debian instead of a heavy rockylinux base, also moved to multi-stage builds
• Tool updates for bcftools, samtools, htslib, deepvariant, GATK, ichorCNA, sigprofiler, vardict
• We have added support for user supplied variables for the variant filtering tasks
• New tools added:
  • CNVear
  • b_pure
• Added PCR Free workflow https://github.com/tgen/tempe/issues/15
• Since alignment must restart, https://github.com/tgen/tempe/issues/17 is handled
• Adjusted support for fasterq files https://github.com/tgen/tempe/issues/24
  • Petagene is only loaded for the copy fastq step and is decompressing the fasterq as part of the copy operation
• Multiple UMI aware alignment updates https://github.com/tgen/tempe/issues/25 https://github.com/tgen/tempe/issues/26 https://github.com/tgen/tempe/issues/27 https://github.com/tgen/tempe/issues/36 https://github.com/tgen/tempe/issues/37
• Adjusted memory usage for a couple of workflows including lancet and deepvariant https://github.com/tgen/tempe/issues/33
  • Deepvariant is using an example of memory request based on the numberOfReads in the sample, this is planned to be expanded upon
• Removed workflows that are outdated/superseded by newer tools:
  • snpEff
  • singleCellRNA support tasks (these will be broken into a separate pipeline in order to reduce workflow complexity)
  • lumosVar
  • CHIP/CutRun alignment and processing