├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── release-checklist.md └── workflows │ ├── docker_cellbrowser.yaml │ ├── docker_vireo-snp.yaml │ ├── nextflow-config-check.yaml │ ├── nextflow-stub-check.yaml │ ├── run-batch.yaml │ └── spell-check.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .vscode └── settings.json ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── air.toml ├── bin ├── add_celltypes_to_sce.R ├── add_demux_sce.R ├── add_infercnv_to_sce.R ├── add_openscpca_annotations.R ├── add_submitter_annotations.R ├── cellbrowser_config.py ├── classify_SingleR.R ├── cluster_sce.R ├── create_cellranger_config.py ├── detect_doublets.R ├── filter_sce.R ├── format_unfiltered_sce.R ├── generate_bulk_metadata.R ├── generate_cellassign_refs.R ├── generate_spaceranger_metadata.R ├── generate_unfiltered_sce_alevin.R ├── generate_unfiltered_sce_cellranger.R ├── integrate_sce.R ├── make_celltype_ref_table.R ├── make_reference_fasta.R ├── merge_sces.R ├── post_process_sce.R ├── predict_cellassign.py ├── prepare_infercnv_gene_order_file.R ├── reformat_anndata.py ├── run_infercnv.R ├── run_scimilarity.py ├── save_singler_refs.R ├── sce_metrics.R ├── sce_qc_report.R ├── sce_to_anndata.R ├── train_SingleR.R └── tximport_bulk.R ├── cavatica-instructions.md ├── cavatica ├── README.md ├── cavatica-build.sh ├── convert-runfile.sh ├── example_run_metadata-cavatica.tsv ├── example_run_metadata.tsv ├── sb_doc.md ├── sb_exclude.txt └── sb_nextflow_schema.yaml ├── components └── dictionary.txt ├── config ├── README.md ├── ccdl_inputs.config ├── ccdl_profiles.config ├── containers.config ├── process_base.config ├── profile_awsbatch.config ├── profile_awsbatch_manual.config ├── profile_example.config ├── profile_stub.config └── reference_paths.config ├── custom-celltype-references.md ├── diagrams └── scpca-nf-overview.png ├── docker ├── README.md ├── cellbrowser │ ├── .dockerignore │ ├── .gitattributes │ ├── .gitignore │ ├── Dockerfile │ ├── pixi.lock │ └── pixi.toml └── vireo-snp │ └── Dockerfile ├── examples ├── README.md ├── example_diagnosis_celltypes.tsv ├── example_multiplex_pools.tsv ├── example_project_celltype_metadata.tsv ├── example_run_metadata.tsv ├── example_sample_metadata.tsv └── user_template.config ├── external-instructions.md ├── get_refs.py ├── internal-instructions.md ├── lib └── Utils.groovy ├── main.nf ├── merge.nf ├── modules ├── af-features.nf ├── af-rna.nf ├── bulk-pileup.nf ├── bulk-salmon.nf ├── bulk-star.nf ├── call-cnvs.nf ├── cellbrowser.nf ├── cellranger-flex.nf ├── cellsnp.nf ├── classify-celltypes.nf ├── cluster-sce.nf ├── export-anndata.nf ├── genetic-demux.nf ├── integrate-sces.nf ├── publish-sce.nf ├── samtools.nf ├── sce-processing.nf ├── spaceranger.nf └── starsolo.nf ├── nextflow.config ├── nextflow_schema.json ├── pixi.lock ├── pixi.toml ├── references ├── PanglaoDB_markers_2020-03-27.tsv ├── README.md ├── celltype-reference-metadata.tsv ├── consensus-cell-type-reference.tsv ├── consensus-validation-groups.tsv ├── diagnosis-celltype-groups.tsv ├── diagnosis-groups.tsv ├── panglao-cell-type-ontologies.tsv ├── ref-metadata.tsv ├── scimilarity-mapped-ontologies.tsv ├── scpca-refs.json ├── scripts │ └── create-reference-json.R └── validation-markers.tsv ├── scripts ├── compare-metrics │ ├── .Rprofile │ ├── compare-metrics-template.rmd │ ├── compare-metrics.R │ ├── renv.lock │ └── renv │ │ ├── .gitignore │ │ ├── activate.R │ │ └── settings.json └── spell-check.R ├── templates ├── cellbrowser │ ├── abstract.html │ ├── cellbrowser.conf │ └── desc.conf ├── merge-report.rmd ├── palettes │ └── validation-group-palette.tsv └── qc_report │ ├── celltypes_qc.rmd │ ├── celltypes_supplemental_report.rmd │ ├── cite_qc.rmd │ ├── infercnv_qc.rmd │ ├── main_qc_report.rmd │ ├── multiplex_qc.rmd │ ├── umap_qc.rmd │ └── utils │ ├── celltype_functions.rmd │ └── report_functions.rmd ├── test ├── .gitignore ├── README.md ├── celltypes │ ├── STUBL01-openscpca-celltypes.json │ └── STUBL12-submitter-celltypes.tsv ├── output │ └── results │ │ └── STUBP01 │ │ ├── STUBS01 │ │ └── STUBL01_processed.rds │ │ └── STUBS16 │ │ └── STUBL16_processed.rds ├── references │ ├── barcodes │ │ ├── 10X │ │ │ ├── 3M-february-2018.txt │ │ │ ├── 737K-august-2016.txt │ │ │ ├── visium-v1.txt │ │ │ └── visium-v2.txt │ │ ├── adt.stub.tsv │ │ └── cellhash.stub.tsv │ ├── celltype │ │ ├── cellassign_references │ │ │ └── cellassign_ref_file.tsv │ │ ├── scimilarity_references │ │ │ └── model_v1.1 │ │ │ │ └── annotation │ │ │ │ └── labelled_kNN.bin │ │ └── singler_models │ │ │ └── singler_model_file.rds │ ├── flex-probe-refs │ │ └── Chromium_Human_Transcriptome_Probe_Set_v1.1.0_GRCh38-2024-A.csv │ ├── infercnv │ │ └── stub_gene_order_arms.txt.gz │ └── stub │ │ ├── annotation │ │ ├── stub.gtf.gz │ │ ├── stub.mitogenes.txt │ │ ├── stub.spliced_cdna.tx2gene.tsv │ │ └── stub.spliced_intron.tx2gene_3col.tsv │ │ ├── cellranger_index │ │ └── stub_cellranger_full │ │ │ └── .gitkeep │ │ ├── fasta │ │ ├── stub.fa.fai │ │ └── stub.fa.gz │ │ ├── infercnv │ │ └── stub_gene_order_arms.txt.gz │ │ ├── salmon_index │ │ ├── stub.spliced_cdna.txome │ │ │ └── .gitkeep │ │ └── stub.spliced_intron.txome │ │ │ └── .gitkeep │ │ └── star_index │ │ └── stub.star_idx │ │ └── .gitkeep ├── runs │ ├── STUBR01 │ │ ├── STUBR01_S1_L001_R1_001.fastq.gz │ │ └── STUBR01_S1_L001_R2_001.fastq.gz │ ├── STUBR02 │ │ ├── STUBR02_S1_L001_R1_001.fastq.gz │ │ └── STUBR02_S1_L001_R2_001.fastq.gz │ ├── STUBR03 │ │ ├── STUBR03_S1_L001_R1_001.fastq.gz │ │ └── STUBR03_S1_L001_R2_001.fastq.gz │ ├── STUBR04 │ │ ├── STUBR04_S1_L001_R1_001.fastq.gz │ │ └── STUBR04_S1_L001_R2_001.fastq.gz │ ├── STUBR05 │ │ ├── STUBR05_S1_L001_R1_001.fastq.gz │ │ └── STUBR05_S1_L001_R2_001.fastq.gz │ ├── STUBR06 │ │ ├── STUBR06_S1_L001_R1_001.fastq.gz │ │ └── STUBR06_S1_L001_R2_001.fastq.gz │ ├── STUBR07 │ │ ├── STUBR07_D1-A-rotate.jpg │ │ ├── STUBR07_S1_L001_R1_001.fastq.gz │ │ └── 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