├── .github └── workflows │ ├── pre_commit.yml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yml ├── LICENSE ├── README.md ├── bin ├── HTODemux-visualisation.R ├── HTODemux.R ├── MultiSeq.R ├── bff.R ├── demuxem.py ├── donor_match.R ├── dropletUtils.R ├── filter_bam_file_for_popscle_dsc_pileup.sh ├── generate_data.py ├── gmm_demux_params.py ├── hashsolo.py ├── pre_processing.R ├── solo_demul.py ├── sort_vcf_same_as_bam.sh ├── summary.py ├── summary_gene.py └── summary_hash.py ├── conda ├── bff.yml ├── demuxem_py.yml ├── donor_match.yml ├── dropletutils.yml ├── gmm_demux.yml ├── hashsolo_py.yml ├── rseurat.yml ├── samtools.yml ├── scsplit.yml ├── solo_py.yml └── summary_py.yml ├── docs ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── _static │ └── images │ │ ├── genotype.png │ │ ├── hashing.png │ │ ├── pipeline.png │ │ └── rescue.png │ ├── conf.py │ ├── general.md │ ├── genetic.md │ ├── hadge_output.ipynb │ ├── hashing.md │ ├── index.md │ ├── multisample.md │ └── rescue.md ├── main.nf ├── modules ├── multi │ ├── donor_match.nf │ ├── gene_demulti │ │ ├── bcftools.nf │ │ ├── cellsnp.nf │ │ ├── demuxlet.nf │ │ ├── freebayes.nf │ │ ├── freemuxlet.nf │ │ ├── samtools.nf │ │ ├── scsplit.nf │ │ ├── souporcell.nf │ │ └── vireo.nf │ ├── gene_demultiplexing.nf │ ├── hash_demulti │ │ ├── bff.nf │ │ ├── demuxem.nf │ │ ├── gmm_demux.nf │ │ ├── hashedDrops.nf │ │ ├── hashsolo.nf │ │ ├── htodemux.nf │ │ ├── multiseq.nf │ │ ├── preprocess.nf │ │ └── solo.nf │ ├── hash_demultiplexing.nf │ └── preprocessing │ │ └── preprocessing.nf └── multi_demultiplexing.nf ├── nextflow.config ├── subworkflows └── HADGE.nf ├── test.config └── test_data ├── download_data.sh ├── hto ├── barcodes.tsv ├── genes.tsv └── matrix.mtx ├── hto_v3 ├── barcodes.tsv.gz ├── features.tsv.gz └── matrix.mtx.gz ├── multi_sample_input.csv ├── rna ├── barcodes.tsv ├── genes.tsv └── matrix.mtx ├── rna_v3 ├── barcodes.tsv.gz ├── features.tsv.gz └── matrix.mtx.gz ├── 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