v20241125

scATAC:

• Output compressed tsv files
• Updated fragment path slot to use relative path
• Added emptyDrops FDR parameter support
• Corrected Q30 explanation mistake
• Output full report metrics as a json file
• Updated docker image building CI workflow

scRNA-seq

• updated docker image building CI workflow

v20241021

• Added 10X style representation of the mean reads per cell metrics in VDJ report and json output

v20240828

• Added reference processing script

v20240823

• Updated scRNA-seq to v1.2.7

v20240725

• Fixed soloCBposition parsing problem

v20240625

scRNA-seq

• Used standard seurat analysis workflow to replace SCTransform, which consumes more memory and is relatively slow
• Used "multicore" to replace "multisession" of future paralell strategy, "multisession" will invoke more threads than required

v20240429

• Added vdj and ATAC pipeline

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
• Added support of custom conda env path (prepared by conda-pack)

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