## What's Changed * Add test configurations by @nictru in https://github.com/nf-core/scdownstream/pull/28 * Add support for CSV input by @nictru in https://github.com/nf-core/scdownstream/pull/30 * Implement harmony integration by @nictru in https://github.com/nf-core/scdownstream/pull/32 * Implement bbknn integration by @nictru in https://github.com/nf-core/scdownstream/pull/33 * Implement combat integration by @nictru in https://github.com/nf-core/scdownstream/pull/34 * Implement seurat integration by @nictru in https://github.com/nf-core/scdownstream/pull/35 * Implement scrublet doublet detection by @nictru in https://github.com/nf-core/scdownstream/pull/36 * Implement doubletdetection doublet detection by @nictru in https://github.com/nf-core/scdownstream/pull/37 * Implement scds doublet detection by @nictru in https://github.com/nf-core/scdownstream/pull/38 * Implement cellbender ambient rna removal by @nictru in https://github.com/nf-core/scdownstream/pull/39 * Implement soupx ambient rna removal by @nictru in https://github.com/nf-core/scdownstream/pull/40 * Implement scar ambient rna removal by @nictru in https://github.com/nf-core/scdownstream/pull/41 * Implement celltypist cell type assignment by @nictru in https://github.com/nf-core/scdownstream/pull/42 * Update documentation of supported ambient RNA removal methods by @nictru in https://github.com/nf-core/scdownstream/pull/43 * Implement custom filtering by @nictru in https://github.com/nf-core/scdownstream/pull/45 * Add citations by @nictru in https://github.com/nf-core/scdownstream/pull/46 * Update docs by @nictru in https://github.com/nf-core/scdownstream/pull/47 * Fix singularity cache problems by @nictru in https://github.com/nf-core/scdownstream/pull/50 * 48 add support for h5 input format by @fbnrst in https://github.com/nf-core/scdownstream/pull/52 * Add support for h5 input format by @nictru in https://github.com/nf-core/scdownstream/pull/54 * Allow skip of ambient_removal by introducing method 'none' by @smoe in https://github.com/nf-core/scdownstream/pull/56 * Use raw cellranger outputs for cellbender by @nictru in https://github.com/nf-core/scdownstream/pull/55 * Add support for background matrix in decontX by @nictru in https://github.com/nf-core/scdownstream/pull/60 * Add parameter for aggregation of duplicate var names by @nictru in https://github.com/nf-core/scdownstream/pull/61 * Implement automatic filtering if only unfiltered matrix is available by @nictru in https://github.com/nf-core/scdownstream/pull/62 * Update schema_input.json: require filtered or unfiltered by @smoe in https://github.com/nf-core/scdownstream/pull/63 * Fix cellbender ch_raw reference by @nictru in https://github.com/nf-core/scdownstream/pull/66 * Fix doublet filtering out non-doublets cells by @nicoaira in https://github.com/nf-core/scdownstream/pull/68 * Implement integration HVG selection by @nictru in https://github.com/nf-core/scdownstream/pull/70 ## New Contributors * @nictru made their first contribution in https://github.com/nf-core/scdownstream/pull/28 * @fbnrst made their first contribution in https://github.com/nf-core/scdownstream/pull/52 * @smoe made their first contribution in https://github.com/nf-core/scdownstream/pull/56 * @nicoaira made their first contribution in https://github.com/nf-core/scdownstream/pull/68 **Full Changelog**: https://github.com/nf-core/scdownstream/commits/v0.0.1