Mini release 2020 Jan - Notebook runner

• Replaced Scanpy report for single cell data analysis with a notebook template

Mini release 2020 Jan - wgs

List of changes

• Added GATK BQSR and HaplotypeCaller GVCF step for alignment pipeline

Pipeline improvements 2020 Jan

List of new improvements:

• changed jobmode of cellranger pipeline from PBSpro to single node
• fixed the remote dir permission issues and enabled UCSC cellbrowser in the primary analysis pipeline

Pipeline improvements 201906

List of new improvements:

• Optimized Ehive pipeline for resource usage and job counts
• New Epigenome QC pipeline with PPQT and Deeptools plots
• New RNA-Seq QC pipeline (with experimental batch effect checking)
• Cellranger for single cell and single nuclei samples
• Scanpy report with 3D UMAP plot for single cell and single nuclei samples
• Bcl2Fastq mask-short-adapter-reads param reset for short read cycles
• Updated doc template
• Using conda yaml file for travis-ci
• Indexing cram output before iRODS upload
• Minor changes added to the metadata db schema
• Fixed security issues for sqlalchemy and jinja versions
• Added a histogram plot in analysis QC page for alignment stats

Pipeline improvements

• Python wrapper scripts moved to data-management-python repo

Single cell demultiplexing pipeline

This release contains the codes required for running the demultiplexing pipeline for single cell runs.

Demultiplexing pipeline

First version of the demuliplexing pipeline.

Initial release

Its the first release of the pipeline codebase.