4.0.0

What's Changed

• Move txp2gene to reference_genome_options in schema as it is required by kb_python and alevin by @matq007 in #434
• Fix additional path splitting for txp2gene by @matq007 in #433
• Add a checker so that --fb_reference does not break the pipeline if ab files are not used in cellranger multi sub-workflow by @fmalmeida in #410
• Fix concatenation of multiple samples into the combined output AnnData by @nictru in #416
• Ensure STARsolo velocity output is added to the combined output AnnData if star_feature = 'Gene Velocyto' by @nictru in #417
• Update cellbender module to latest nf-core version by @fmalmeida in #419
• Add profile for GPU processes by @fmalmeida in #419
• Update example usage command in README with valid reference genome parameter by @kopichris in #414
• Remove --kb_filter parameter, by @fmalmeida in #422
• Improvements in cellbender documentation by @fmalmeida in #423
• Add --limitBAMsortRAM to STARsolo alignment to ensure BAM sorting memory scales with task memory by @nictru in #430
• Replace local modules for simpleaf, SIMPLEAF_INDEX, and SIMPLEAF_QUANT with centralized nf-core modules, updating simpleaf sub-workflows accordingly by @DongzeHE in #424
• Update documentation for simpleaf, alevin, salmon, and alevin-fry for consistency by @DongzeHE in #424
• Rename the default aligner from alevin to simpleaf for consistency by @DongzeHE in #424
• Update mtx_to_h5ad template for simpleaf to use the h5ad file generated by simpleaf by @DongzeHE in #424
• Upgrade alevinQC from 1.12.1 to 1.18.0 to match the latest simpleaf output structure by @DongzeHE in #424

See also the CHANGELOG.

New Contributors

• @DongzeHE made their first contribution in #424

Full Changelog: 3.0.0...4.0.0