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Overhaul and quantification workflow
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@acesnik acesnik released this 02 Aug 16:48
· 16 commits to master since this release
0.3.3
f8498af

Overhaul and quantification workflow

  • IMPORTANT FOR GUI USAGE: This release requires .NET 5.0. Please download the .NET Runtime here https://dotnet.microsoft.com/download/dotnet/5.0.
  • IMPORTANT FOR CMD USAGE: Please update your conda environment to make sure .NET 5.0 runtime is available.

New features:

  • Using conda environments for every rule to allow snakemake --use-conda to be more efficient if a subset of workflows is selected
  • Adding quick quantification with StringTie2 of both assembled isoforms and reference transcripts, and summarizing the quant results in a table
  • New SpritzCMD commandline interface that wraps snakemake for usage in a base conda environment

Bug fixes:

  • This fixes an issue with TransferUniProtModifications (#215)

Other improvements:

  • TransferUniProtModifications now named SpritzModifications
  • Removed duplicate biopython reference
  • Restructuring folders according to https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html
  • Removed -SO coordinate from AddReadGroups in variant workflow because it looks like that triggers a followup sort
  • Allocated double GATK's normal RAM to MarkDuplicates because it runs close to the RAM limit
  • Removing fusion workflow, since it's not integrated and I don't have plans to do so in the near future
  • Removed aspera-cli because SRA-prefetch isn't really using it but still getting 10x faster downloads with HTTPS than fasterq-dump
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