├── .dockerignore ├── .dockstore.yml ├── .gcloudignore ├── .gitattributes ├── .gitignore ├── .vimrc ├── LICENSE ├── README.md ├── cloudbuild.yaml ├── dockerfiles ├── 10x_task_preprocess.dockerfile ├── dorcs_task_find_dorcs.dockerfile ├── notes-for-bowtie ├── share_task_archr.dockerfile ├── share_task_bowtie2.dockerfile ├── share_task_cell_annotation.dockerfile ├── share_task_correct_fastq.dockerfile ├── share_task_filter_atac.dockerfile ├── share_task_generate_h5.dockerfile ├── share_task_html_report.dockerfile ├── share_task_joint_qc.dockerfile ├── share_task_merge_bams.dockerfile ├── share_task_preprocess.dockerfile ├── share_task_qc_atac.dockerfile ├── share_task_qc_rna.dockerfile ├── share_task_seurat.dockerfile ├── share_task_star.dockerfile ├── share_task_trim_fastqs_atac.dockerfile └── terra_archr_and_seurat.dockerfile ├── docs ├── images │ └── pipeline_overview.png ├── input.md └── input_short.md ├── example_input_json ├── inputs-complete-share.json ├── inputs-complete-shareseq.json ├── inputs-short-share.json └── subwf_preprocess.json ├── share-seq.wdl ├── src ├── R │ ├── DORCS_helper_functions_optimized.R │ ├── TSSRanges.RData │ ├── atac_qc_plots.R │ ├── barcode_rank_functions.R │ ├── cell_annotation.R │ ├── cell_annotation_helper_functions.R │ ├── joint_cell_plotting_density.R │ └── rna_qc_plots.R ├── bash │ └── monitor_script.sh ├── jupyter_nb │ ├── archr_notebook.ipynb │ ├── cell_annotation_notebook.ipynb │ ├── dorcs_jplot_notebook.ipynb │ └── seurat_notebook.ipynb └── python │ ├── assign_multimappers.py │ ├── bam_fastq.py │ ├── bam_to_fragments.py │ ├── bam_to_raw_fastq.py │ ├── barcode_revcomp_detect.py │ ├── correct_fastq.py │ ├── detect_multiplets.py │ ├── filter_mito_reads.py │ ├── flexible_import_entities_standard.py │ ├── generate_h5_rna.py │ ├── get_cellxgene_data.py │ ├── infer_barcodes.py │ ├── joint_cell_plotting.py │ ├── match_barcodes.py │ ├── pbc_stats.py │ ├── plot_insert_size_hist.py │ ├── qc_atac_compute_reads_in_peaks.py │ ├── qc_atac_compute_tss_enrichment.py │ ├── qc_atac_count_duplicates_per_barcode.py │ ├── rna_barcode_metadata.py │ ├── trim_fastq.py │ ├── write_html.py │ └── write_terra_tables.py ├── tasks ├── 10x_create_barcode_mapping.wdl ├── 10x_task_preprocess.wdl ├── dorcs_task_find_dorcs.wdl ├── get_cellxgene_data.wdl ├── raise_exception.wdl ├── share_task_archr.wdl ├── share_task_bowtie2.wdl ├── share_task_cell_annotation.wdl ├── share_task_correct_fastq.wdl ├── share_task_filter_atac.wdl ├── share_task_generate_h5.wdl ├── share_task_html_report.wdl ├── share_task_joint_qc.wdl ├── share_task_log_atac.wdl ├── share_task_log_rna.wdl ├── share_task_merge_bams.wdl ├── share_task_qc_atac.wdl ├── share_task_qc_rna.wdl ├── share_task_seurat.wdl ├── share_task_star.wdl ├── share_task_starsolo.wdl └── share_task_trim_fastqs_atac.wdl └── workflows ├── subwf-atac-archr.wdl ├── subwf-atac.wdl ├── subwf-cell-annotation.wdl ├── subwf-find-dorcs.wdl ├── 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