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  • Also simplification in version checking (now just marked in GUI code)
  • Uses updated minimamba docker container
6cc01ae
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Fix SpritzModifications issue on Ubuntu

  • Added quotes and equals characters for arguments for SpritzModifications.dll
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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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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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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
fcf95eb
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50bf754
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0.2.4

updates mzlib package, fixes a build error (#200)
ff86cf5
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  • Added ability to use single-end FASTQs
  • Added ability to use single-end SRAs
  • Added ability to use mixed single-end and paired-end inputs
  • Added ability to use mixed SRA and FASTQ inputs
  • Improved ease of commandline usage
31d66a2
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  • This release includes an installer and an autoupdater to stay up to date.
  • Can select either/both variant and isoform (beta) workflows
  • Speedier trimming tool
  • Many other changes