v2.3.0

Fix

• Output schema with correct expression matrix paths.

Added

• Spatial plotting of visium data in workflow report for genes specified by --genes_of_interest.

Changed

• The genes to be used for annotating UMAP plots are now specified by --genes_of_interest.
• Updated Ezcharts to v0.11.2.

v2.2.0

Added

• Alignment summary section to report.
• Support for 10x 3prime v4 (GEM-X) (--kit 3prime:v4).

v2.1.0

Changed

• Options --kit_name and --kit_version replaced with single option --kit (eg --kit 3prime:v3)

Added

• Error handling when empty expression matrix is created.

v2.0.3

Fixed

• Error when a tags file is empty

Added

• More informative error message when all cells or features are filtered out.

v2.0.2

Fixed

• Mito gene counts all being zero.

Changed

• Skip publishing of gibberish mito-transcript count file.

Added

• Note to README concerning singularity temporary directory.

v2.0.0

Fixed

• Reported cell count off by -1 in report summary table.
• Issue with TSV concat/splitting during combine_bam_and_tags stage.
• Issue introduced in v1.1.0 that caused a partial BAM file to be output.
• Corrected example command in README.
• Incorrect reporting of unique gene and transcripts in report table.
• Processed expression matrix entries incorrectly filtered.
• Gene identity of multimapping reads could be incorrectly assigned.

Changed

• Read chunking done in library code.
• --process_chunk_size parameter changed to --fastq_chunk
• Resource declarations in Nextflow processes.
• Simplified read batching and decoupled from CPU usage parameters.
• Expression matrix construction code reworked to reduce memory usage.
• Adapter search step now 3x faster.
• Barcode assignment 3x faster.
• Feature assignment now 15x faster.
• UMI clustering 20x faster.
• UMAP creation memory use reduced 6-fold and up-to 30x faster (and
  always enabled).
• Final read tagging step is 3x faster.
• Combined various preprocessing steps into a single process to avoid
  unnecessary file writes.
• Updated stringtie2 to v2.2.2.
• Pre-calculate report summary data to reduce disk-space and IO overheads.
• Single BAM per-sample is now always produced (option --merge_bam is removed).

Removed

• Several workflow parameters as part of resource management simplification.
• --plot_umaps option, as UMAP generation has been made much more efficient
  and is always enabled.
• --merge_bam option.

v1.1.0

Added

• full_length_only parameter to process only full length reads (default: true).
• Trim adapters, barcodes and UMIs from reads before alignment.
• Memory directive for umap process to prevent parallel processes from using too much memory.

Changed

• Orient 3prime/multiome reads to mRNA sense to avoid need to flip later.
• Default umap_n_repeats lowered to 3.
• Genome reference alignment done by chunk.

Fixed

• Issue where splice junctions were searched for on incorrect strand.

v1.0.3

Added

• Publish stringtie transcriptome fasta and GFF files to output dir.

Fixed

• More informative error message upon read duplicate detection.

Updated

• Remove duplicate fastcat call.

v1.0.1

Fixed

• <img> tags in the docs.

v1.0.0

Updated

• Docs to the new format.