Quantification summary fix

0.3.13

update both versions (#242)

Uniprot downloader and versioning fixes

Fix version (#235)

* fix loaders

* fix download workflow

* finishing touches'

* revert version

* improve ensembl release listing

* versioning

* versioning fix

---------

Co-authored-by: Anthony Cesnik <cesnik@stanford.edu>

Uniprot downloader fixes

0.3.9

Update RunnerEngine.cs version

Installer update

use httpclient (#227)

* use httpclient

* installer stuff

* spaces

Uniprot download fix

0.3.7

Update RunnerEngine.cs

Uniprot download fix

Update mzLib to fix issue downloading psimod (#225)

* Update mzLib to fix issue downloading psimod

* edit github and docker files

* update net 6.0 in workflow

* update version & one more net version change

* use legacy

* downloadup

Fix docker building

• Also simplification in version checking (now just marked in GUI code)
• Uses updated minimamba docker container

Fix SpritzModifications issue on Ubuntu

Fix SpritzModifications issue on Ubuntu

• Added quotes and equals characters for arguments for SpritzModifications.dll

Overhaul and quantification workflow

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

Overhaul and quantification workflow

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