v1.2.9

• Updated docker image building workflow

v1.1.8

• Updated VDJ filtration criteria when only BCR/TCR library was used
• VDJ library barcodes will be filtered by cells identified in GEX library
• Minor bug fixed for VDJ pipeline
• Constrained fastqc>=0.11.9 cutadapt>=3.5in conda yml file
• VDJ pipeline will publish trust4 report and airr file now
• Fixed barcodelist bug when invoking complex barcode pipeline for BD style barcode

v1.1.6

• Updated saturation script to include data as preseqR input
• Updated VDJ subworkflow to adapt to the new library structure
• Fix the feature_types bug for VDJ report process
• Added GEX association section to the VDJ report

v1.1.3

Added --outBAMsortingBinsN 300 option to STARsolo process to solve the RAM issue when sorting a very large BAM file, refer to STAR #870

v1.1.2

updated to v1.1.2

v1.1.1

• Added memory setup in the report process
• Added option for publishing starsolo BAM output

v1.1.0 VDJ pipeline added

• Added VDJ workflow (GEX+VDJ)
• Removed time limit for process resources
• Modified the margin of the tables in the 3'-scRNA-Seq report
• Adjusted knee plot to fixed size and center positioned

v1.0.0

• Added pipeline running information to the reports
• Fixed issue for saturation calculation script when there is no whitelist provided
• Output a full list of DEGs

v0.0.9

• Updated STAR to v2.7.10a in both the docker image and the conda environment
• Adapt the pipeline to generate report for starsolo --soloMultiMappers option, only "Unique" and "EM" are supported by now.
• Changed the default parameter for --soloFeatures to "GeneFull", which includes both exon and intron reads

v0.0.7

• Raw gene/barcode count table will be stored in a loom file and published for subsequent analysis
• Mapping metrics will be written to a json file
• Added support for 5' RNA-seq library