KFDRC RNAseq Production Workflow

What's Changed

• 🚸 Optional inputs for Cavatica Batch Tasks by @dmiller15 in #37

Full Changelog: v4.0.0...v4.1.0

🎉 KFDRC RNAseq Workflow V4 Release

This is a mild refactor of our RNAseq workflow. All of the same tools that you know and love are still there, but have been upgraded to new versions. Also, our default gene model (GENCODE27) has been upgraded (to GENCODE39) and will be applied to all of our cohorts in the near future.

Version changes:

• Cutadapt: 2.5 -> 3.4
• STAR: 2.6.1d -> 2.7.10a
• STAR-Fusion: 1.5.0 -> 1.10.1
• Arriba: 1.1.0 -> 2.2.1

Other notes

• Genomic bam output will now be cram output, transcriptome bam is now omitted. Plan accordingly.
• STAR run parameters have been tuned to arriba-recommended, but are highly customizable

KFDRC RNAseq Production Workflow

Hotfix for the previous release. Fixes an issue where the nameext check for gzipped files in STAR align was missing a .

What's Changed

• 🐛 star nameext failure by @dmiller15 in #32

Full Changelog: v3.0.0...v3.0.1

KFDRC RNAseq Production Workflow

What's Changed

• 🎉 add rmats by @dmiller15 in #31

Added rMATS workflow and integrated the workflow into the production RNAseq workflow.

Full Changelog: v2.4.2...v3.0.0

Minor aesthetic and compatibility updates

1. Updated strand parse tool to take advantage of native enum and dump throw on error
2. Moved deprecated workflow wrapper to avoid confusion
3. Updated cwl in samtools_fastq to be compatible with cwltool and sbg suggested value in annofuse for sbpack compatibility

KFDRC RNAseq Production Workflow

Bug fix with new suggested file paths.

KFDRC RNAseq Production Workflow

This release updates the dockerPulls for all tools that were using a DockerHub registry.

KFDRC RNAseq Production Workflow

Input Clarification:

• Clearly delineated difference between sample_name and output_basename inputs. The latter is used in file names; the former is used within the contents of the file.

KFDRC RNAseq Production Workflow

This release adds annoFuse to the main RNAseq workflow

Functional changes:

• Adds annoFuse workflow to main RNAseq workflow
• Updates annoFuse tools to 0.90.0
• Changes num_col default in annoFuse from 25 to 24

Documentation:

• Updates readme with changes to main workflow and annoFuse version
• Updates image for RNAseq workflow

KFDRC RNAseq Production Workflow

This release fixes a bug in the public apps so that the files point to publicly available ID's.