4.2.0

What's Changed

• Update to cellranger v10.0.0 by @tgelafr-pfzr in #508
• Fix bug with probeset and index mismatch when using cellranger multi with a probeset and without a pre-built index by @tgelafr-pfzr in #502
• handle BOM files, update test to include BOM by @tgelafr-pfzr in #511
• #512: Validate cellranger multi barcode sheet early by @tgelafr-pfzr in #513
• Improve modules.config structure by @nictru in #514
• 515: Fix bug processing singleplex flex data by @tgelafr-pfzr in #517
• Important! Template update for nf-core/tools v3.5.1 by @nf-core-bot in #509
• Fix #522: Protocol processing for cellrangermulti by @tgelafr-pfzr in #524
• Fix FASTQC filename collisions by @tgelafr-pfzr in #535
• Replace alevinqc with qcatch for simpleaf QC by @an-altosian in #520
• Fix strict syntax errors by @bentsherman in #536
• Remove duplicate process_gpu config section by @heuermh in #537
• Important! Template update for nf-core/tools v4.0.2 by @nf-core-bot in #541
• Use bioconductor-anndatar v1.0.0 by @lazappi in #472
• Fix genome handling by @nictru in #545
• Overwrite null values for param inputs using igenomes by @tgelafr-pfzr in #548
• Prepare 4.2.0 release by @nictru in #550
• Create per-subworkflow directories by @nictru in #553
• Re-route megatests slack notifications to #scrnaseq-dev slack channel by @nictru in #551
• Fix remaining linting warnings by @nictru in #542
• Star igenomes compatibility by @nictru in #552
• Cellranger gtf space incompatibility by @nictru in #554
• Nftignore flaky test bam by @nictru in #557
• Fix remaining AWS test issues by @nictru in #556
• feat(qcatch): nest qcatch_protocol, expose n_partitions, run QCatch for all simpleaf protocols by @an-altosian in #560
• Fix/prepare genome optional fasta and gtf by @nictru in #562
• Remove empty Unreleased section from CHANGELOG by @nictru in #561
• 4.2.0 release by @nictru in #558

New Contributors

• @tgelafr-pfzr made their first contribution in #508
• @bentsherman made their first contribution in #536
• @heuermh made their first contribution in #537
• @lazappi made their first contribution in #472

Full Changelog: 4.1.0...4.2.0