├── .circleci └── config.yml ├── .gitignore ├── .pullapprove.yml ├── CHANGELOG.md ├── LICENSE ├── README.md ├── benchmarking ├── optimus │ ├── REPRODUCE.rst │ ├── media │ │ ├── image1.png │ │ ├── image10.png │ │ ├── image11.png │ │ ├── image12.png │ │ ├── image13.png │ │ ├── image14.png │ │ ├── image15.png │ │ ├── image16.png │ │ ├── image17.png │ │ ├── image18.png │ │ ├── image19.png │ │ ├── image2.png │ │ ├── image20.png │ │ ├── image21.png │ │ ├── image22.png │ │ ├── image23.png │ │ ├── image24.png │ │ ├── image25.png │ │ ├── image26.png │ │ ├── image27.png │ │ ├── image28.png │ │ ├── image29.png │ │ ├── image3.png │ │ ├── image30.png │ │ ├── image31.png │ │ ├── image32.png │ │ ├── image33.png │ │ ├── image34.png │ │ ├── image35.png │ │ ├── image36.png │ │ ├── image37.png │ │ ├── image38.png │ │ ├── image39.png │ │ ├── image4.png │ │ ├── image40.png │ │ ├── image41.png │ │ ├── image42.png │ │ ├── image43.png │ │ ├── image44.png │ │ ├── image45.png │ │ ├── image46.png │ │ ├── image47.png │ │ ├── image48.png │ │ ├── image49.png │ │ ├── image5.png │ │ ├── image50.png │ │ ├── image51.png │ │ ├── image52.png │ │ ├── image53.png │ │ ├── image54.png │ │ ├── image55.png │ │ ├── image56.png │ │ ├── image57.png │ │ ├── image58.png │ │ ├── image59.png │ │ ├── image6.png │ │ ├── image60.png │ │ ├── image61.png │ │ ├── image62.png │ │ ├── image63.png │ │ ├── image64.png │ │ ├── image65.png │ │ ├── image7.png │ │ ├── image8.png │ │ └── image9.png │ └── optimus_report.rst └── smartseq2 │ ├── BenchmarkingTasks.wdl │ ├── R │ ├── Compare_Quantification.R │ ├── Compare_data_matrix.R │ ├── Confounding_factor_analysis.R │ ├── QC_metrics_analysis.R │ ├── analysis_functions.R │ ├── combine_QC_quant_metrics.R │ └── data_matrix_reproducibility.R │ ├── RunBenchmarkingAnalysis.json │ └── RunBenchmarkingAnalysis.wdl ├── docker ├── analysis-tools │ └── Dockerfile ├── benchmarking-tools │ └── Dockerfile ├── cellranger │ ├── Dockerfile │ ├── README.md │ └── requirements.txt ├── dropseq_tools │ └── Dockerfile ├── dropseq_tools_v2 │ ├── Dockerfile │ └── build.sh ├── emptydrops │ ├── Dockerfile │ ├── build.sh │ ├── emptyDropsWrapper │ │ ├── README.md │ │ ├── emptyDropsWrapper.R │ │ └── test │ │ │ ├── prepRDS.R │ │ │ └── test_emptyDropsWrapper.sh │ ├── installRDeps.R │ └── npz2rds │ │ ├── README.md │ │ ├── npz2rds.sh │ │ ├── npz2txt.py │ │ ├── sparseTxt2Rds.R │ │ └── test │ │ ├── input.tar.gz │ │ └── test.sh ├── gtfToGenePred │ └── Dockerfile ├── hisat2 │ └── Dockerfile ├── kallisto │ └── Dockerfile ├── loom-output │ ├── Dockerfile │ ├── build.sh │ ├── create_loom_optimus.py │ ├── create_loom_ss2.py │ ├── loomCompare.py │ ├── requirements.txt │ └── ss2_loom_merge.py ├── modify-gtf │ ├── Dockerfile │ ├── SetGeneNameToId.py │ └── build.sh ├── optimus-test-matrix │ ├── Dockerfile │ ├── build.sh │ ├── checkMatrix.R │ ├── installRDeps.R │ └── npz2rds │ │ ├── README.md │ │ ├── npz2rds.sh │ │ ├── npz2txt.py │ │ ├── sparseTxt2Rds.R │ │ └── test │ │ ├── input.tar.gz │ │ └── test.sh ├── patched-star │ └── Dockerfile ├── picard │ └── Dockerfile ├── rsem │ └── Dockerfile ├── samtools │ └── Dockerfile ├── snap-breakout │ ├── Dockerfile │ ├── breakoutSnap.py │ └── build.sh ├── snaptools │ ├── Dockerfile │ ├── build.sh │ └── makeCompliantBAM.py ├── star │ └── Dockerfile ├── subread │ └── Dockerfile ├── subset-fastq-dataset │ ├── Dockerfile │ ├── build.sh │ └── filterFastqByReadName.py └── umi-tools │ ├── Dockerfile │ ├── build.sh │ └── getUntaggedReads ├── docs └── matrix_format_spec.md ├── library ├── accessory_workflows │ ├── build_bwa_reference │ │ ├── bwa-mk-index.wdl │ │ └── inputs-example.json │ ├── build_cellranger_reference │ │ ├── BuildCellRangerReferenceBundle.wdl │ │ ├── BuildCellRangerReferenceBundleEnsembl.json │ │ └── BuildCellRangerReferenceBundleGencode.json │ ├── build_indices │ │ ├── BuildIndices.wdl │ │ ├── README.md │ │ ├── human_inputs.json │ │ └── mouse_inputs.json │ ├── kallisto_mkref.wdl │ ├── scatter_workflows │ │ ├── run_pipeline.wdl │ │ ├── run_pipeline_ind.wdl │ │ ├── run_pipeline_scatter.wdl │ │ └── run_pipeline_test.json │ ├── subset_fastq_dataset │ │ └── subset_fastq_dataset.wdl │ └── testing_workflows │ │ ├── SmartSeq2SingleSampleHISAT2.wdl │ │ ├── SmartSeq2SingleSampleStar.wdl │ │ ├── kallisto_pipeline.wdl │ │ ├── kallisto_pipeline_test.json │ │ ├── run_pipeline_tests.json │ │ └── run_pipeline_tests.wdl └── tasks │ ├── Attach10xBarcodes.wdl │ ├── CollectMultiplePicardMetrics.wdl │ ├── CorrectUmiMarkDuplicates.wdl │ ├── CreateCountMatrix.wdl │ ├── FastqToUBam.wdl │ ├── GroupMetricsOutputs.wdl │ ├── HISAT2.wdl │ ├── Kallisto.wdl │ ├── LoomUtils.wdl │ ├── MergeSortBam.wdl │ ├── ModifyGtf.wdl │ ├── OptimusInputChecks.wdl │ ├── Picard.wdl │ ├── RSEM.wdl │ ├── RunEmptyDrops.wdl │ ├── SS2InputChecks.wdl │ ├── ScatterBam.wdl │ ├── SequenceDataWithMoleculeTagMetrics.wdl │ ├── SplitBamByCellBarcode.wdl │ ├── StarAlignBamSingleEnd.wdl │ ├── StarAlignFastqSingleEnd.wdl │ ├── StarMkref.wdl │ ├── TagGeneExon.wdl │ ├── TagSortBam.wdl │ ├── UmiCorrection.wdl │ ├── featurecounts.wdl │ ├── htseq.wdl │ └── star.wdl ├── pipelines ├── 10x │ ├── README.md │ ├── count │ │ ├── README.md │ │ ├── count.wdl │ │ └── example_count_input.json │ ├── docker-10x │ │ ├── Dockerfile │ │ ├── README.md │ │ └── run_in_10x_env.bash │ ├── generate_demo_data │ │ ├── README.md │ │ ├── generate_demo_data.wdl │ │ ├── generate_demo_data_example_inputs.json │ │ └── generate_demo_data_example_inputs2.json │ ├── generate_reference_bundle │ │ ├── README.md │ │ ├── generate_reference_bundle.wdl │ │ └── generate_reference_bundle_example_inputs.json │ ├── martian_README.md │ └── wdls │ │ ├── example_make_fastq_input.json │ │ └── make_fastq.wdl ├── bulk_rna_pipeline │ ├── Readme.md │ ├── bulk_rna_pipeline.wdl │ └── test_inputs.json ├── cellranger │ ├── cellranger.wdl │ └── test_inputs.json ├── optimus │ ├── Bam_tags.md │ ├── Loom_schema.md │ ├── Optimus.changelog.md │ ├── Optimus.wdl │ ├── Optimus_diagram.png │ ├── Optimus_diagram.pptx │ ├── Optimus_pipeline_overview.png │ ├── README.md │ ├── human_v2_example.json │ ├── human_v3_example.json │ ├── mouse_v2_example.json │ ├── mouse_v2_snRNA_example.json │ └── test_optimus_full_datasets │ │ ├── README.MD │ │ ├── inputs_4k_panT_cells.json │ │ ├── inputs_4k_pbmc.json │ │ ├── inputs_8k_pbmc.json │ │ ├── inputs_BM1_HiSeq_1.json │ │ ├── inputs_BM1_HiSeq_2.json │ │ ├── inputs_BM2_HiSeq_1.json │ │ ├── inputs_CB1_HiSeq_1.json │ │ ├── inputs_CB2_HiSeq_1.json │ │ ├── inputs_cd8_cytotoxic_t_cells.json │ │ ├── inputs_ischaemic_sensitivity_1.json │ │ ├── inputs_ischaemic_sensitivity_2.json │ │ ├── inputs_ischaemic_sensitivity_3.json │ │ ├── inputs_ischaemic_sensitivity_4.json │ │ └── inputs_ischaemic_sensitivity_5.json ├── scATAC │ ├── ATAC.inputs.json │ ├── ATAC.options.json │ ├── ATAC.wdl │ └── SplitFastq ├── smartseq2_multisample │ ├── Loom_schema.md │ ├── MultiSampleSmartSeq2.changelog.md │ ├── MultiSampleSmartSeq2.wdl │ ├── README.md │ ├── dependency.json │ ├── human_single_example.json │ └── mouse_paired_example.json ├── smartseq2_single_sample │ ├── Creating_Smartseq2_References.md │ ├── Loom_schema.md │ ├── README.md │ ├── SmartSeq2SingleSample.changelog.md │ ├── SmartSeq2SingleSample.wdl │ ├── human_single_example.json │ ├── labels.json │ ├── mouse_paired_example.json │ ├── options.json │ ├── smartseq_image.png │ └── smartseq_image.pptx └── snap-atac │ ├── README.md │ ├── human_example.json │ ├── scATAC.changelog.md │ ├── scATAC.wdl │ └── scATAC_diagram.png ├── pull_request_template.md ├── security.txt └── test ├── README.md ├── bulk_rna_pipeline └── pr │ ├── ValidateBulkRna.wdl │ ├── dependencies.json │ ├── test_bulk_rna_pipeline_PR.wdl │ └── test_inputs.json ├── config ├── cromwell-secrets.json.ctmpl └── render-ctmpls.sh ├── optimus ├── 4kpbmc │ ├── dependencies.json │ ├── test_inputs.json │ └── test_optimus_4KPBMC.wdl ├── pr │ ├── ValidateOptimus.wdl │ ├── dependencies.json │ ├── test_inputs.json │ └── test_optimus_PR.wdl └── prV3 │ ├── dependencies.json │ ├── test_inputs.json │ └── test_optimus_PRV3.wdl ├── optimus_mouse └── pr │ ├── ValidateOptimusMouse.wdl │ ├── dependencies.json │ ├── test_inputs.json │ └── test_optimus_mouse_PR.wdl ├── optimus_snrna ├── 2kBrainNucleiAdultMouse │ ├── dependencies.json │ ├── test_inputs.json │ └── test_optimus_snrna_2KBRAINNUCLEIADULTMOUSE.wdl ├── 4kpbmc_manual │ ├── dependencies.json │ ├── test_inputs.json │ └── test_optimus_snrna_4KPBMC_MANUAL.wdl └── pr │ ├── dependencies.json │ ├── test_inputs.json │ └── test_optimus_snrna_PR.wdl ├── options.json ├── run_portability_test.py ├── sc_atac └── pr │ ├── ValidateSCATAC.wdl │ ├── dependencies.json │ ├── test_inputs.json │ └── test_sc_atac_PR.wdl ├── smartseq2_multisample ├── pr │ ├── ValidateMultiSampleSmartSeq2.wdl │ ├── dependencies.json │ ├── test_inputs.json │ └── test_smartseq2_multisample_PR.wdl └── pr_single_end │ ├── ValidateMultiSampleSmartSeq2.wdl │ ├── dependencies.json │ ├── test_inputs.json │ └── test_smartseq2_multisample_PR_SINGLE_END.wdl ├── smartseq2_single_sample ├── pr │ ├── ValidateSmartSeq2SingleCell.wdl │ ├── dependencies.json │ ├── test_inputs.json │ └── test_smartseq2_single_sample_PR.wdl └── pr_single_end │ ├── ValidateSmartSeq2SingleCell.wdl │ ├── dependencies.json │ ├── test_inputs.json │ └── test_smartseq2_single_sample_PR_SINGLE_END.wdl ├── snap_atac └── pr │ ├── ValidateSnapATAC.wdl │ ├── dependencies.json │ ├── test_inputs.json │ └── test_snap_atac_PR.wdl ├── test_cromwell_workflow.sh ├── test_pr_tests.ipynb ├── trigger_cellranger_test.sh ├── trigger_scientific_test.sh └── trigger_test.sh /.circleci/config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/.circleci/config.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/.gitignore -------------------------------------------------------------------------------- /.pullapprove.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/.pullapprove.yml -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/CHANGELOG.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/README.md -------------------------------------------------------------------------------- /benchmarking/optimus/REPRODUCE.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/REPRODUCE.rst -------------------------------------------------------------------------------- /benchmarking/optimus/media/image1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image1.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image10.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image10.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image11.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image11.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image12.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image12.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image13.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image13.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image14.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image14.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image15.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image15.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image16.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image16.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image17.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image17.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image18.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image18.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image19.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image19.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image2.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image20.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image20.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image21.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image21.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image22.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image22.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image23.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image23.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image24.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image24.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image25.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image25.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image26.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image26.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image27.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image27.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image28.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image28.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image29.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image29.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image3.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image30.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image30.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image31.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image31.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image32.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image32.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image33.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image33.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image34.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image34.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image35.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image35.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image36.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image36.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image37.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image37.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image38.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image38.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image39.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image39.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image4.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image40.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image40.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image41.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image41.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image42.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image42.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image43.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image43.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image44.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image44.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image45.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image45.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image46.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image46.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image47.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image47.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image48.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image48.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image49.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image49.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image5.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image5.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image50.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image50.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image51.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image51.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image52.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image52.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image53.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image53.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image54.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image54.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image55.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image55.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image56.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image56.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image57.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image57.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image58.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image58.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image59.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image59.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image6.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image6.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image60.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image60.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image61.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image61.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image62.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image62.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image63.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image63.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image64.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image64.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image65.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image65.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image7.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image7.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image8.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image8.png -------------------------------------------------------------------------------- /benchmarking/optimus/media/image9.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/media/image9.png -------------------------------------------------------------------------------- /benchmarking/optimus/optimus_report.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/optimus/optimus_report.rst -------------------------------------------------------------------------------- /benchmarking/smartseq2/BenchmarkingTasks.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/smartseq2/BenchmarkingTasks.wdl -------------------------------------------------------------------------------- /benchmarking/smartseq2/R/Compare_Quantification.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/smartseq2/R/Compare_Quantification.R -------------------------------------------------------------------------------- /benchmarking/smartseq2/R/Compare_data_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/smartseq2/R/Compare_data_matrix.R -------------------------------------------------------------------------------- /benchmarking/smartseq2/R/Confounding_factor_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/smartseq2/R/Confounding_factor_analysis.R -------------------------------------------------------------------------------- /benchmarking/smartseq2/R/QC_metrics_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/smartseq2/R/QC_metrics_analysis.R -------------------------------------------------------------------------------- /benchmarking/smartseq2/R/analysis_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/smartseq2/R/analysis_functions.R -------------------------------------------------------------------------------- /benchmarking/smartseq2/R/combine_QC_quant_metrics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/smartseq2/R/combine_QC_quant_metrics.R -------------------------------------------------------------------------------- /benchmarking/smartseq2/R/data_matrix_reproducibility.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/smartseq2/R/data_matrix_reproducibility.R -------------------------------------------------------------------------------- /benchmarking/smartseq2/RunBenchmarkingAnalysis.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/smartseq2/RunBenchmarkingAnalysis.json -------------------------------------------------------------------------------- /benchmarking/smartseq2/RunBenchmarkingAnalysis.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/benchmarking/smartseq2/RunBenchmarkingAnalysis.wdl -------------------------------------------------------------------------------- /docker/analysis-tools/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/analysis-tools/Dockerfile -------------------------------------------------------------------------------- /docker/benchmarking-tools/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/benchmarking-tools/Dockerfile -------------------------------------------------------------------------------- /docker/cellranger/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/cellranger/Dockerfile -------------------------------------------------------------------------------- /docker/cellranger/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/cellranger/README.md -------------------------------------------------------------------------------- /docker/cellranger/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/cellranger/requirements.txt -------------------------------------------------------------------------------- /docker/dropseq_tools/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/dropseq_tools/Dockerfile -------------------------------------------------------------------------------- /docker/dropseq_tools_v2/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/dropseq_tools_v2/Dockerfile -------------------------------------------------------------------------------- /docker/dropseq_tools_v2/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/dropseq_tools_v2/build.sh -------------------------------------------------------------------------------- /docker/emptydrops/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/Dockerfile -------------------------------------------------------------------------------- /docker/emptydrops/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/build.sh -------------------------------------------------------------------------------- /docker/emptydrops/emptyDropsWrapper/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/emptyDropsWrapper/README.md -------------------------------------------------------------------------------- /docker/emptydrops/emptyDropsWrapper/emptyDropsWrapper.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/emptyDropsWrapper/emptyDropsWrapper.R -------------------------------------------------------------------------------- /docker/emptydrops/emptyDropsWrapper/test/prepRDS.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/emptyDropsWrapper/test/prepRDS.R -------------------------------------------------------------------------------- /docker/emptydrops/emptyDropsWrapper/test/test_emptyDropsWrapper.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/emptyDropsWrapper/test/test_emptyDropsWrapper.sh -------------------------------------------------------------------------------- /docker/emptydrops/installRDeps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/installRDeps.R -------------------------------------------------------------------------------- /docker/emptydrops/npz2rds/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/npz2rds/README.md -------------------------------------------------------------------------------- /docker/emptydrops/npz2rds/npz2rds.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/npz2rds/npz2rds.sh -------------------------------------------------------------------------------- /docker/emptydrops/npz2rds/npz2txt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/npz2rds/npz2txt.py -------------------------------------------------------------------------------- /docker/emptydrops/npz2rds/sparseTxt2Rds.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/npz2rds/sparseTxt2Rds.R -------------------------------------------------------------------------------- /docker/emptydrops/npz2rds/test/input.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/npz2rds/test/input.tar.gz -------------------------------------------------------------------------------- /docker/emptydrops/npz2rds/test/test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/emptydrops/npz2rds/test/test.sh -------------------------------------------------------------------------------- /docker/gtfToGenePred/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/gtfToGenePred/Dockerfile -------------------------------------------------------------------------------- /docker/hisat2/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/hisat2/Dockerfile -------------------------------------------------------------------------------- /docker/kallisto/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/kallisto/Dockerfile -------------------------------------------------------------------------------- /docker/loom-output/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/loom-output/Dockerfile -------------------------------------------------------------------------------- /docker/loom-output/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/loom-output/build.sh -------------------------------------------------------------------------------- /docker/loom-output/create_loom_optimus.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/loom-output/create_loom_optimus.py -------------------------------------------------------------------------------- /docker/loom-output/create_loom_ss2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/loom-output/create_loom_ss2.py -------------------------------------------------------------------------------- /docker/loom-output/loomCompare.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/loom-output/loomCompare.py -------------------------------------------------------------------------------- /docker/loom-output/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/loom-output/requirements.txt -------------------------------------------------------------------------------- /docker/loom-output/ss2_loom_merge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/loom-output/ss2_loom_merge.py -------------------------------------------------------------------------------- /docker/modify-gtf/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/modify-gtf/Dockerfile -------------------------------------------------------------------------------- /docker/modify-gtf/SetGeneNameToId.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/modify-gtf/SetGeneNameToId.py -------------------------------------------------------------------------------- /docker/modify-gtf/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/modify-gtf/build.sh -------------------------------------------------------------------------------- /docker/optimus-test-matrix/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/optimus-test-matrix/Dockerfile -------------------------------------------------------------------------------- /docker/optimus-test-matrix/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/optimus-test-matrix/build.sh -------------------------------------------------------------------------------- /docker/optimus-test-matrix/checkMatrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/optimus-test-matrix/checkMatrix.R -------------------------------------------------------------------------------- /docker/optimus-test-matrix/installRDeps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/optimus-test-matrix/installRDeps.R -------------------------------------------------------------------------------- /docker/optimus-test-matrix/npz2rds/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/optimus-test-matrix/npz2rds/README.md -------------------------------------------------------------------------------- /docker/optimus-test-matrix/npz2rds/npz2rds.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/optimus-test-matrix/npz2rds/npz2rds.sh -------------------------------------------------------------------------------- /docker/optimus-test-matrix/npz2rds/npz2txt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/optimus-test-matrix/npz2rds/npz2txt.py -------------------------------------------------------------------------------- /docker/optimus-test-matrix/npz2rds/sparseTxt2Rds.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/optimus-test-matrix/npz2rds/sparseTxt2Rds.R -------------------------------------------------------------------------------- /docker/optimus-test-matrix/npz2rds/test/input.tar.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/optimus-test-matrix/npz2rds/test/input.tar.gz -------------------------------------------------------------------------------- /docker/optimus-test-matrix/npz2rds/test/test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/optimus-test-matrix/npz2rds/test/test.sh -------------------------------------------------------------------------------- /docker/patched-star/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/patched-star/Dockerfile -------------------------------------------------------------------------------- /docker/picard/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/picard/Dockerfile -------------------------------------------------------------------------------- /docker/rsem/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/rsem/Dockerfile -------------------------------------------------------------------------------- /docker/samtools/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/samtools/Dockerfile -------------------------------------------------------------------------------- /docker/snap-breakout/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/snap-breakout/Dockerfile -------------------------------------------------------------------------------- /docker/snap-breakout/breakoutSnap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/snap-breakout/breakoutSnap.py -------------------------------------------------------------------------------- /docker/snap-breakout/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/snap-breakout/build.sh -------------------------------------------------------------------------------- /docker/snaptools/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/snaptools/Dockerfile -------------------------------------------------------------------------------- /docker/snaptools/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/snaptools/build.sh -------------------------------------------------------------------------------- /docker/snaptools/makeCompliantBAM.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/snaptools/makeCompliantBAM.py -------------------------------------------------------------------------------- /docker/star/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/star/Dockerfile -------------------------------------------------------------------------------- /docker/subread/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/subread/Dockerfile -------------------------------------------------------------------------------- /docker/subset-fastq-dataset/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/subset-fastq-dataset/Dockerfile -------------------------------------------------------------------------------- /docker/subset-fastq-dataset/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/subset-fastq-dataset/build.sh -------------------------------------------------------------------------------- /docker/subset-fastq-dataset/filterFastqByReadName.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/subset-fastq-dataset/filterFastqByReadName.py -------------------------------------------------------------------------------- /docker/umi-tools/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/umi-tools/Dockerfile -------------------------------------------------------------------------------- /docker/umi-tools/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/umi-tools/build.sh -------------------------------------------------------------------------------- /docker/umi-tools/getUntaggedReads: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docker/umi-tools/getUntaggedReads -------------------------------------------------------------------------------- /docs/matrix_format_spec.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/docs/matrix_format_spec.md -------------------------------------------------------------------------------- /library/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/build_bwa_reference/bwa-mk-index.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/build_bwa_reference/inputs-example.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/build_bwa_reference/inputs-example.json -------------------------------------------------------------------------------- /library/accessory_workflows/build_cellranger_reference/BuildCellRangerReferenceBundle.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/build_cellranger_reference/BuildCellRangerReferenceBundle.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/build_cellranger_reference/BuildCellRangerReferenceBundleEnsembl.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/build_cellranger_reference/BuildCellRangerReferenceBundleEnsembl.json -------------------------------------------------------------------------------- /library/accessory_workflows/build_cellranger_reference/BuildCellRangerReferenceBundleGencode.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/build_cellranger_reference/BuildCellRangerReferenceBundleGencode.json -------------------------------------------------------------------------------- /library/accessory_workflows/build_indices/BuildIndices.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/build_indices/BuildIndices.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/build_indices/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/build_indices/README.md -------------------------------------------------------------------------------- /library/accessory_workflows/build_indices/human_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/build_indices/human_inputs.json -------------------------------------------------------------------------------- /library/accessory_workflows/build_indices/mouse_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/build_indices/mouse_inputs.json -------------------------------------------------------------------------------- /library/accessory_workflows/kallisto_mkref.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/kallisto_mkref.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/scatter_workflows/run_pipeline.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/scatter_workflows/run_pipeline.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/scatter_workflows/run_pipeline_ind.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/scatter_workflows/run_pipeline_ind.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/scatter_workflows/run_pipeline_scatter.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/scatter_workflows/run_pipeline_scatter.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/scatter_workflows/run_pipeline_test.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/scatter_workflows/run_pipeline_test.json -------------------------------------------------------------------------------- /library/accessory_workflows/subset_fastq_dataset/subset_fastq_dataset.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/subset_fastq_dataset/subset_fastq_dataset.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/testing_workflows/SmartSeq2SingleSampleHISAT2.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/testing_workflows/SmartSeq2SingleSampleHISAT2.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/testing_workflows/SmartSeq2SingleSampleStar.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/testing_workflows/SmartSeq2SingleSampleStar.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/testing_workflows/kallisto_pipeline.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/testing_workflows/kallisto_pipeline.wdl -------------------------------------------------------------------------------- /library/accessory_workflows/testing_workflows/kallisto_pipeline_test.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/testing_workflows/kallisto_pipeline_test.json -------------------------------------------------------------------------------- /library/accessory_workflows/testing_workflows/run_pipeline_tests.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/testing_workflows/run_pipeline_tests.json -------------------------------------------------------------------------------- /library/accessory_workflows/testing_workflows/run_pipeline_tests.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/accessory_workflows/testing_workflows/run_pipeline_tests.wdl -------------------------------------------------------------------------------- /library/tasks/Attach10xBarcodes.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/Attach10xBarcodes.wdl -------------------------------------------------------------------------------- /library/tasks/CollectMultiplePicardMetrics.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/CollectMultiplePicardMetrics.wdl -------------------------------------------------------------------------------- /library/tasks/CorrectUmiMarkDuplicates.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/CorrectUmiMarkDuplicates.wdl -------------------------------------------------------------------------------- /library/tasks/CreateCountMatrix.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/CreateCountMatrix.wdl -------------------------------------------------------------------------------- /library/tasks/FastqToUBam.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/FastqToUBam.wdl -------------------------------------------------------------------------------- /library/tasks/GroupMetricsOutputs.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/GroupMetricsOutputs.wdl -------------------------------------------------------------------------------- /library/tasks/HISAT2.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/HISAT2.wdl -------------------------------------------------------------------------------- /library/tasks/Kallisto.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/Kallisto.wdl -------------------------------------------------------------------------------- /library/tasks/LoomUtils.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/LoomUtils.wdl -------------------------------------------------------------------------------- /library/tasks/MergeSortBam.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/MergeSortBam.wdl -------------------------------------------------------------------------------- /library/tasks/ModifyGtf.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/ModifyGtf.wdl -------------------------------------------------------------------------------- /library/tasks/OptimusInputChecks.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/OptimusInputChecks.wdl -------------------------------------------------------------------------------- /library/tasks/Picard.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/Picard.wdl -------------------------------------------------------------------------------- /library/tasks/RSEM.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/RSEM.wdl -------------------------------------------------------------------------------- /library/tasks/RunEmptyDrops.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/RunEmptyDrops.wdl -------------------------------------------------------------------------------- /library/tasks/SS2InputChecks.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/SS2InputChecks.wdl -------------------------------------------------------------------------------- /library/tasks/ScatterBam.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/ScatterBam.wdl -------------------------------------------------------------------------------- /library/tasks/SequenceDataWithMoleculeTagMetrics.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/SequenceDataWithMoleculeTagMetrics.wdl -------------------------------------------------------------------------------- /library/tasks/SplitBamByCellBarcode.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/SplitBamByCellBarcode.wdl -------------------------------------------------------------------------------- /library/tasks/StarAlignBamSingleEnd.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/StarAlignBamSingleEnd.wdl -------------------------------------------------------------------------------- /library/tasks/StarAlignFastqSingleEnd.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/StarAlignFastqSingleEnd.wdl -------------------------------------------------------------------------------- /library/tasks/StarMkref.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/StarMkref.wdl -------------------------------------------------------------------------------- /library/tasks/TagGeneExon.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/TagGeneExon.wdl -------------------------------------------------------------------------------- /library/tasks/TagSortBam.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/TagSortBam.wdl -------------------------------------------------------------------------------- /library/tasks/UmiCorrection.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/UmiCorrection.wdl -------------------------------------------------------------------------------- /library/tasks/featurecounts.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/featurecounts.wdl -------------------------------------------------------------------------------- /library/tasks/htseq.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/htseq.wdl -------------------------------------------------------------------------------- /library/tasks/star.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/library/tasks/star.wdl -------------------------------------------------------------------------------- /pipelines/10x/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/README.md -------------------------------------------------------------------------------- /pipelines/10x/count/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/count/README.md -------------------------------------------------------------------------------- /pipelines/10x/count/count.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/count/count.wdl -------------------------------------------------------------------------------- /pipelines/10x/count/example_count_input.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/count/example_count_input.json -------------------------------------------------------------------------------- /pipelines/10x/docker-10x/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/docker-10x/Dockerfile -------------------------------------------------------------------------------- /pipelines/10x/docker-10x/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/docker-10x/README.md -------------------------------------------------------------------------------- /pipelines/10x/docker-10x/run_in_10x_env.bash: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/docker-10x/run_in_10x_env.bash -------------------------------------------------------------------------------- /pipelines/10x/generate_demo_data/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/generate_demo_data/README.md -------------------------------------------------------------------------------- /pipelines/10x/generate_demo_data/generate_demo_data.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/generate_demo_data/generate_demo_data.wdl -------------------------------------------------------------------------------- /pipelines/10x/generate_demo_data/generate_demo_data_example_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/generate_demo_data/generate_demo_data_example_inputs.json -------------------------------------------------------------------------------- /pipelines/10x/generate_demo_data/generate_demo_data_example_inputs2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/generate_demo_data/generate_demo_data_example_inputs2.json -------------------------------------------------------------------------------- /pipelines/10x/generate_reference_bundle/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/generate_reference_bundle/README.md -------------------------------------------------------------------------------- /pipelines/10x/generate_reference_bundle/generate_reference_bundle.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/generate_reference_bundle/generate_reference_bundle.wdl -------------------------------------------------------------------------------- /pipelines/10x/generate_reference_bundle/generate_reference_bundle_example_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/generate_reference_bundle/generate_reference_bundle_example_inputs.json -------------------------------------------------------------------------------- /pipelines/10x/martian_README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/martian_README.md -------------------------------------------------------------------------------- /pipelines/10x/wdls/example_make_fastq_input.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/wdls/example_make_fastq_input.json -------------------------------------------------------------------------------- /pipelines/10x/wdls/make_fastq.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/10x/wdls/make_fastq.wdl -------------------------------------------------------------------------------- /pipelines/bulk_rna_pipeline/Readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/bulk_rna_pipeline/Readme.md -------------------------------------------------------------------------------- /pipelines/bulk_rna_pipeline/bulk_rna_pipeline.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/bulk_rna_pipeline/bulk_rna_pipeline.wdl -------------------------------------------------------------------------------- /pipelines/bulk_rna_pipeline/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/bulk_rna_pipeline/test_inputs.json -------------------------------------------------------------------------------- /pipelines/cellranger/cellranger.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/cellranger/cellranger.wdl -------------------------------------------------------------------------------- /pipelines/cellranger/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/cellranger/test_inputs.json -------------------------------------------------------------------------------- /pipelines/optimus/Bam_tags.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/Bam_tags.md -------------------------------------------------------------------------------- /pipelines/optimus/Loom_schema.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/Loom_schema.md -------------------------------------------------------------------------------- /pipelines/optimus/Optimus.changelog.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/Optimus.changelog.md -------------------------------------------------------------------------------- /pipelines/optimus/Optimus.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/Optimus.wdl -------------------------------------------------------------------------------- /pipelines/optimus/Optimus_diagram.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/Optimus_diagram.png -------------------------------------------------------------------------------- /pipelines/optimus/Optimus_diagram.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/Optimus_diagram.pptx -------------------------------------------------------------------------------- /pipelines/optimus/Optimus_pipeline_overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/Optimus_pipeline_overview.png -------------------------------------------------------------------------------- /pipelines/optimus/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/README.md -------------------------------------------------------------------------------- /pipelines/optimus/human_v2_example.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/human_v2_example.json -------------------------------------------------------------------------------- /pipelines/optimus/human_v3_example.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/human_v3_example.json -------------------------------------------------------------------------------- /pipelines/optimus/mouse_v2_example.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/mouse_v2_example.json -------------------------------------------------------------------------------- /pipelines/optimus/mouse_v2_snRNA_example.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/mouse_v2_snRNA_example.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/README.MD: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/README.MD -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_4k_panT_cells.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_4k_panT_cells.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_4k_pbmc.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_4k_pbmc.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_8k_pbmc.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_8k_pbmc.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_BM1_HiSeq_1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_BM1_HiSeq_1.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_BM1_HiSeq_2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_BM1_HiSeq_2.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_BM2_HiSeq_1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_BM2_HiSeq_1.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_CB1_HiSeq_1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_CB1_HiSeq_1.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_CB2_HiSeq_1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_CB2_HiSeq_1.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_cd8_cytotoxic_t_cells.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_cd8_cytotoxic_t_cells.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_ischaemic_sensitivity_1.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_ischaemic_sensitivity_1.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_ischaemic_sensitivity_2.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_ischaemic_sensitivity_2.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_ischaemic_sensitivity_3.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_ischaemic_sensitivity_3.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_ischaemic_sensitivity_4.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_ischaemic_sensitivity_4.json -------------------------------------------------------------------------------- /pipelines/optimus/test_optimus_full_datasets/inputs_ischaemic_sensitivity_5.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/optimus/test_optimus_full_datasets/inputs_ischaemic_sensitivity_5.json -------------------------------------------------------------------------------- /pipelines/scATAC/ATAC.inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/scATAC/ATAC.inputs.json -------------------------------------------------------------------------------- /pipelines/scATAC/ATAC.options.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/scATAC/ATAC.options.json -------------------------------------------------------------------------------- /pipelines/scATAC/ATAC.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/scATAC/ATAC.wdl -------------------------------------------------------------------------------- /pipelines/scATAC/SplitFastq: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/scATAC/SplitFastq -------------------------------------------------------------------------------- /pipelines/smartseq2_multisample/Loom_schema.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_multisample/Loom_schema.md -------------------------------------------------------------------------------- /pipelines/smartseq2_multisample/MultiSampleSmartSeq2.changelog.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_multisample/MultiSampleSmartSeq2.changelog.md -------------------------------------------------------------------------------- /pipelines/smartseq2_multisample/MultiSampleSmartSeq2.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_multisample/MultiSampleSmartSeq2.wdl -------------------------------------------------------------------------------- /pipelines/smartseq2_multisample/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_multisample/README.md -------------------------------------------------------------------------------- /pipelines/smartseq2_multisample/dependency.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_multisample/dependency.json -------------------------------------------------------------------------------- /pipelines/smartseq2_multisample/human_single_example.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_multisample/human_single_example.json -------------------------------------------------------------------------------- /pipelines/smartseq2_multisample/mouse_paired_example.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_multisample/mouse_paired_example.json -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/Creating_Smartseq2_References.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/Creating_Smartseq2_References.md -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/Loom_schema.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/Loom_schema.md -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/README.md -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/SmartSeq2SingleSample.changelog.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/SmartSeq2SingleSample.changelog.md -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/SmartSeq2SingleSample.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/SmartSeq2SingleSample.wdl -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/human_single_example.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/human_single_example.json -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/labels.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/labels.json -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/mouse_paired_example.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/mouse_paired_example.json -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/options.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/options.json -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/smartseq_image.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/smartseq_image.png -------------------------------------------------------------------------------- /pipelines/smartseq2_single_sample/smartseq_image.pptx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/smartseq2_single_sample/smartseq_image.pptx -------------------------------------------------------------------------------- /pipelines/snap-atac/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/snap-atac/README.md -------------------------------------------------------------------------------- /pipelines/snap-atac/human_example.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/snap-atac/human_example.json -------------------------------------------------------------------------------- /pipelines/snap-atac/scATAC.changelog.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/snap-atac/scATAC.changelog.md -------------------------------------------------------------------------------- /pipelines/snap-atac/scATAC.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/snap-atac/scATAC.wdl -------------------------------------------------------------------------------- /pipelines/snap-atac/scATAC_diagram.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pipelines/snap-atac/scATAC_diagram.png -------------------------------------------------------------------------------- /pull_request_template.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/pull_request_template.md -------------------------------------------------------------------------------- /security.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/security.txt -------------------------------------------------------------------------------- /test/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/README.md -------------------------------------------------------------------------------- /test/bulk_rna_pipeline/pr/ValidateBulkRna.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/bulk_rna_pipeline/pr/ValidateBulkRna.wdl -------------------------------------------------------------------------------- /test/bulk_rna_pipeline/pr/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/bulk_rna_pipeline/pr/dependencies.json -------------------------------------------------------------------------------- /test/bulk_rna_pipeline/pr/test_bulk_rna_pipeline_PR.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/bulk_rna_pipeline/pr/test_bulk_rna_pipeline_PR.wdl -------------------------------------------------------------------------------- /test/bulk_rna_pipeline/pr/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/bulk_rna_pipeline/pr/test_inputs.json -------------------------------------------------------------------------------- /test/config/cromwell-secrets.json.ctmpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/config/cromwell-secrets.json.ctmpl -------------------------------------------------------------------------------- /test/config/render-ctmpls.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/config/render-ctmpls.sh -------------------------------------------------------------------------------- /test/optimus/4kpbmc/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus/4kpbmc/dependencies.json -------------------------------------------------------------------------------- /test/optimus/4kpbmc/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus/4kpbmc/test_inputs.json -------------------------------------------------------------------------------- /test/optimus/4kpbmc/test_optimus_4KPBMC.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus/4kpbmc/test_optimus_4KPBMC.wdl -------------------------------------------------------------------------------- /test/optimus/pr/ValidateOptimus.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus/pr/ValidateOptimus.wdl -------------------------------------------------------------------------------- /test/optimus/pr/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus/pr/dependencies.json -------------------------------------------------------------------------------- /test/optimus/pr/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus/pr/test_inputs.json -------------------------------------------------------------------------------- /test/optimus/pr/test_optimus_PR.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus/pr/test_optimus_PR.wdl -------------------------------------------------------------------------------- /test/optimus/prV3/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus/prV3/dependencies.json -------------------------------------------------------------------------------- /test/optimus/prV3/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus/prV3/test_inputs.json -------------------------------------------------------------------------------- /test/optimus/prV3/test_optimus_PRV3.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus/prV3/test_optimus_PRV3.wdl -------------------------------------------------------------------------------- /test/optimus_mouse/pr/ValidateOptimusMouse.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_mouse/pr/ValidateOptimusMouse.wdl -------------------------------------------------------------------------------- /test/optimus_mouse/pr/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_mouse/pr/dependencies.json -------------------------------------------------------------------------------- /test/optimus_mouse/pr/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_mouse/pr/test_inputs.json -------------------------------------------------------------------------------- /test/optimus_mouse/pr/test_optimus_mouse_PR.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_mouse/pr/test_optimus_mouse_PR.wdl -------------------------------------------------------------------------------- /test/optimus_snrna/2kBrainNucleiAdultMouse/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_snrna/2kBrainNucleiAdultMouse/dependencies.json -------------------------------------------------------------------------------- /test/optimus_snrna/2kBrainNucleiAdultMouse/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_snrna/2kBrainNucleiAdultMouse/test_inputs.json -------------------------------------------------------------------------------- /test/optimus_snrna/2kBrainNucleiAdultMouse/test_optimus_snrna_2KBRAINNUCLEIADULTMOUSE.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_snrna/2kBrainNucleiAdultMouse/test_optimus_snrna_2KBRAINNUCLEIADULTMOUSE.wdl -------------------------------------------------------------------------------- /test/optimus_snrna/4kpbmc_manual/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_snrna/4kpbmc_manual/dependencies.json -------------------------------------------------------------------------------- /test/optimus_snrna/4kpbmc_manual/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_snrna/4kpbmc_manual/test_inputs.json -------------------------------------------------------------------------------- /test/optimus_snrna/4kpbmc_manual/test_optimus_snrna_4KPBMC_MANUAL.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_snrna/4kpbmc_manual/test_optimus_snrna_4KPBMC_MANUAL.wdl -------------------------------------------------------------------------------- /test/optimus_snrna/pr/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_snrna/pr/dependencies.json -------------------------------------------------------------------------------- /test/optimus_snrna/pr/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_snrna/pr/test_inputs.json -------------------------------------------------------------------------------- /test/optimus_snrna/pr/test_optimus_snrna_PR.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/optimus_snrna/pr/test_optimus_snrna_PR.wdl -------------------------------------------------------------------------------- /test/options.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/options.json -------------------------------------------------------------------------------- /test/run_portability_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/run_portability_test.py -------------------------------------------------------------------------------- /test/sc_atac/pr/ValidateSCATAC.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/sc_atac/pr/ValidateSCATAC.wdl -------------------------------------------------------------------------------- /test/sc_atac/pr/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/sc_atac/pr/dependencies.json -------------------------------------------------------------------------------- /test/sc_atac/pr/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/sc_atac/pr/test_inputs.json -------------------------------------------------------------------------------- /test/sc_atac/pr/test_sc_atac_PR.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/sc_atac/pr/test_sc_atac_PR.wdl -------------------------------------------------------------------------------- /test/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_multisample/pr/ValidateMultiSampleSmartSeq2.wdl -------------------------------------------------------------------------------- /test/smartseq2_multisample/pr/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_multisample/pr/dependencies.json -------------------------------------------------------------------------------- /test/smartseq2_multisample/pr/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_multisample/pr/test_inputs.json -------------------------------------------------------------------------------- /test/smartseq2_multisample/pr/test_smartseq2_multisample_PR.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_multisample/pr/test_smartseq2_multisample_PR.wdl -------------------------------------------------------------------------------- /test/smartseq2_multisample/pr_single_end/ValidateMultiSampleSmartSeq2.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_multisample/pr_single_end/ValidateMultiSampleSmartSeq2.wdl -------------------------------------------------------------------------------- /test/smartseq2_multisample/pr_single_end/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_multisample/pr_single_end/dependencies.json -------------------------------------------------------------------------------- /test/smartseq2_multisample/pr_single_end/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_multisample/pr_single_end/test_inputs.json -------------------------------------------------------------------------------- /test/smartseq2_multisample/pr_single_end/test_smartseq2_multisample_PR_SINGLE_END.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_multisample/pr_single_end/test_smartseq2_multisample_PR_SINGLE_END.wdl -------------------------------------------------------------------------------- /test/smartseq2_single_sample/pr/ValidateSmartSeq2SingleCell.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_single_sample/pr/ValidateSmartSeq2SingleCell.wdl -------------------------------------------------------------------------------- /test/smartseq2_single_sample/pr/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_single_sample/pr/dependencies.json -------------------------------------------------------------------------------- /test/smartseq2_single_sample/pr/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_single_sample/pr/test_inputs.json -------------------------------------------------------------------------------- /test/smartseq2_single_sample/pr/test_smartseq2_single_sample_PR.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_single_sample/pr/test_smartseq2_single_sample_PR.wdl -------------------------------------------------------------------------------- /test/smartseq2_single_sample/pr_single_end/ValidateSmartSeq2SingleCell.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_single_sample/pr_single_end/ValidateSmartSeq2SingleCell.wdl -------------------------------------------------------------------------------- /test/smartseq2_single_sample/pr_single_end/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_single_sample/pr_single_end/dependencies.json -------------------------------------------------------------------------------- /test/smartseq2_single_sample/pr_single_end/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_single_sample/pr_single_end/test_inputs.json -------------------------------------------------------------------------------- /test/smartseq2_single_sample/pr_single_end/test_smartseq2_single_sample_PR_SINGLE_END.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/smartseq2_single_sample/pr_single_end/test_smartseq2_single_sample_PR_SINGLE_END.wdl -------------------------------------------------------------------------------- /test/snap_atac/pr/ValidateSnapATAC.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/snap_atac/pr/ValidateSnapATAC.wdl -------------------------------------------------------------------------------- /test/snap_atac/pr/dependencies.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/snap_atac/pr/dependencies.json -------------------------------------------------------------------------------- /test/snap_atac/pr/test_inputs.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/snap_atac/pr/test_inputs.json -------------------------------------------------------------------------------- /test/snap_atac/pr/test_snap_atac_PR.wdl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/snap_atac/pr/test_snap_atac_PR.wdl -------------------------------------------------------------------------------- /test/test_cromwell_workflow.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/test_cromwell_workflow.sh -------------------------------------------------------------------------------- /test/test_pr_tests.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/test_pr_tests.ipynb -------------------------------------------------------------------------------- /test/trigger_cellranger_test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/trigger_cellranger_test.sh -------------------------------------------------------------------------------- /test/trigger_scientific_test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/trigger_scientific_test.sh -------------------------------------------------------------------------------- /test/trigger_test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HumanCellAtlas/skylab/HEAD/test/trigger_test.sh --------------------------------------------------------------------------------