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.

v0.3.0

Fixed

• single_cell_sample_sheet samples with same kit name and version not compatible.

Changed

-exp_cells to expected_cells in single_cell_sample_sheet to be consistent with CLI option.

v0.2.9

• Make prepare_report_data process more memory-efficient

v0.2.8

Fixed

• Increase the maximum memory available to the adapter_scan process
• Fix sequence truncation by 1 bp in adapter_scan step
• Make summarize_adapter_table process more memory-efficient

v0.2.7

Fixed

• Mitochondrial expression file not being copied to output directory
• Incorrect setting of polars maximum threads

Added

• Allow geneName attribute in GTF annotation file

v0.2.6

Fixed

• Alignments generated from 5' 10x kit are now in the correct orientation.

v0.2.5

Added

• Memory directives to some processes to better manage system resources

Changed

• Bumped minimum required Nextflow version to 22.10.8
• GitHub issue templates
• Add chunking of input data to some processes to reduce memory usage

Fixed

• Output BAM files with alignments from incorrect chromosomes
• Incorrect uncorrected_barcodes.tsv output