pipeline_june_2024

What's Changed

• Analysis feb24 by @avikdatta in #81

Full Changelog: 2.1...2.2

pipeline_jan_2024

• Move to Airflow v2.6.2
• Updates for analysis pipelines

pipeline_June_2023

Pipelines running on Airflow v2.2.2

Mini release 2020 Jan - Notebook runner

List of changes

• Added a module to run jupyter nbconvert within singularity container
• Replaced Scanpy report for single cell data analysis with a notebook

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:

• changes in the metadata schema of igfdb for the following tables
  • project
  • platform
  • experiment
  • user
• added a wrapper script for running singularity bases tool
• updated metadata requirements for pipeline
• added codes for reformatting the metadata and samplesheet files
• updated metadata validation codes
• fixed the remote dir permission issues and enabled UCSC cellbrowser in the primary analysis pipeline

Pipeline improvements 201906

List of new improvements:

• 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 201805

List of new improvements:

• A script for changing project barcode checking
• A script for resetting sampleheet info for pipeline after modification
• A script for resetting demultiplexing pipeline for specific set of sequencing runs
• A script for fetching library information from sample attribute tables and populating the experiment records
• Fixed project data display page access for non-hpc users by skipping ldap based login authentication
• Fixed image size of the project display page and calculating the height based on number of samples for each projects
• Logging the exact Bcl2Fastq command to Slack and Asana for future reference
• Added new methods to the ProjectAdaptor module for fetching and counting sample records for a specific project
• Capitalizing user name before entering to database
• Passing executable path for sendmail to the account registration script via parameter

Pipeline improvements 201804

List of new improvements:

• Python wrapper scripts moved from igf-pipeline repo
• Added new unique constraint for Run table
• Bugfix for metadata checks while finding new metadata or sequencing runs
• Added validation checks for samplesheet data

Single cell demultiplexing pipeline

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