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Upgrade the image to the OCI Format or Docker Image manifest v2, schema 2 ?

Status: Open.

#42 In UCSC-Treehouse/pipelines;

· Noepiga opened on Mar 27, 2026

Add parameter to run expression only with RSEM and parameter to run QC

Status: Open.

#41 In UCSC-Treehouse/pipelines;

· Noepiga opened on Mar 19, 2026

pre-check for write permissions before processing (Treeshop)

Status: Open.

#40 In UCSC-Treehouse/pipelines;

· e-t-k opened on Aug 9, 2023

How to handle failed fusion runs?

Status: Open.

#38 In UCSC-Treehouse/pipelines;

· e-t-k opened on Oct 27, 2022

Pipeline does not support expanded FASTQ files, only gzipped

Status: Open.

#37 In UCSC-Treehouse/pipelines;

· e-t-k opened on Oct 21, 2022

Pipeline does not support single end

Status: Open.

#36 In UCSC-Treehouse/pipelines;

· e-t-k opened on Oct 21, 2022

pizzly crashes when run directly from Makefile

Status: Open.

#34 In UCSC-Treehouse/pipelines;

· e-t-k opened on Jun 5, 2019

Update fusion docker version

Status: Open.

#32 In UCSC-Treehouse/pipelines;

· e-t-k opened on May 30, 2019

Custom tweak for CCLE compute: no fusion / bam download

Status: Open.

#26 In UCSC-Treehouse/pipelines;

· e-t-k opened on Feb 5, 2019

Add FLT3-ITD Pipeline

Status: Open.

#25 In UCSC-Treehouse/pipelines;

· jpfeil opened on Jan 30, 2019

Makefile: should crash when finding N>2 fastq files

Status: Open.

#21 In UCSC-Treehouse/pipelines;

· e-t-k opened on Oct 2, 2018

Explore lite pipeline

Status: Open.

#20 In UCSC-Treehouse/pipelines;

· rcurrie opened on Jul 25, 2018