#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: InlineJavascriptRequirement: {} MultipleInputFeatureRequirement: {} inputs: running_step: type: int inputBinding: position: 1 loadDataR: type: File inputBinding: position: 2 barcodes: type: File inputBinding: position: 3 features: type: File inputBinding: position: 4 matrix: type: File inputBinding: position: 5 minCells: type: int inputBinding: position: 6 minFeatures: type: int inputBinding: position: 7 projectName: type: string inputBinding: position: 8 pattern: type: string inputBinding: position: 9 filterDataR: type: File inputBinding: position: 10 nFeatureRNAmin: type: string inputBinding: position: 11 nFeatureRNAmax: type: string inputBinding: position: 12 nCountRNAmin: type: string inputBinding: position: 13 nCountRNAmax: type: string inputBinding: position: 14 percentMTmin: type: string inputBinding: position: 15 percentMTmax: type: string inputBinding: position: 16 normalizeDataR: type: File inputBinding: position: 17 normalization_method: type: string inputBinding: position: 18 scale_factor: type: string inputBinding: position: 19 margin: type: string inputBinding: position: 20 block_size: type: string inputBinding: position: 21 verbose: type: string inputBinding: position: 22 featureSelectionDataR: type: File inputBinding: position: 23 selection_method: type: string inputBinding: position: 24 loess_span: type: string inputBinding: position: 25 clip_max: type: string inputBinding: position: 26 num_bin: type: string inputBinding: position: 27 binning_method: type: string inputBinding: position: 28 num_features: type: string inputBinding: position: 29 scaleDataR: type: File inputBinding: position: 30 runPCAR: type: File inputBinding: position: 31 findNeighborsR: type: File inputBinding: position: 32 neighbors_method: type: string inputBinding: position: 33 k: type: string inputBinding: position: 34 clusterDataR: type: File inputBinding: position: 35 runUmapR: type: File inputBinding: position: 36 runTSNER: type: File inputBinding: position: 37 find_markersR: type: File inputBinding: position: 38 outputs: loadDataOutput: type: File outputSource: loadData/loaded_data loadDataPlot: type: File outputSource: loadData/data_plot filterDataOutput: type: File outputSource: filterData/filtered_data filterDataPlot: type: File outputSource: filterData/filtered_data_plot normalizeDataOutput: type: File outputSource: normalizeData/normalized_data findFeaturesOutput: type: File outputSource: findFeatures/find_features_data findFeaturesPlot: type: File outputSource: findFeatures/features_data_plot scaleDataOutput: type: File outputSource: scaleData/scaling_data runPCAOutput: type: File outputSource: runPCA/pca_data runPCAPlot1: type: File outputSource: runPCA/pca_1_plot runPCAPlot2: type: File outputSource: runPCA/pca_2_plot runPCAPlot3: type: File outputSource: runPCA/pca_3_plot findNeighborsOutput: type: File outputSource: findNeighbors/find_neighbors clusterDataOutput: type: File outputSource: clusterData/cluster_data runUMAPOutput: type: File outputSource: runUMAP/run_umap_data runUMAPOutputPlot: type: File outputSource: runUMAP/run_umap_data_plot runTSNEOutput: type: File outputSource: runTSNE/run_tsne_data findMarkersOutput: type: File outputSource: findAllMarkers/find_markers steps: loadData: in: script: loadDataR barcodes: barcodes features: features matrix: matrix minCells: minCells minFeatures: minFeatures projectName: projectName pattern: pattern run: tools/1_loadData.cwl out: [loaded_data,data_plot] filterData: run: tools/2_filter.cwl in: script: filterDataR dataFile: loadData/loaded_data nFeatureRNAmin: nFeatureRNAmin nFeatureRNAmax: nFeatureRNAmax nCountRNAmin: nCountRNAmin nCountRNAmax: nCountRNAmax percentMTmin: percentMTmin percentMTmax: percentMTmax out: [filtered_data,filtered_data_plot] normalizeData: run: tools/3_normalization.cwl in: script: normalizeDataR dataFile: filterData/filtered_data normalization_method: normalization_method scale_factor: scale_factor margin: margin block_size: block_size verbose: verbose out: [normalized_data] findFeatures: run: tools/4_featureSelection.cwl in: script: featureSelectionDataR dataFile: normalizeData/normalized_data selection_method: selection_method loess_span: loess_span clip_max: clip_max num_bin: num_bin binning_method: binning_method nfeatures: num_features out: [find_features_data,features_data_plot] scaleData: run: tools/5_Scaling.cwl in: script: scaleDataR dataFile: findFeatures/find_features_data out: [scaling_data] runPCA: run: tools/6_PCA.cwl in: script: runPCAR dataFile: scaleData/scaling_data out: [pca_data, pca_1_plot, pca_2_plot, pca_3_plot] findNeighbors: run: tools/7_findNeighbors.cwl in: script: findNeighborsR dataFile: runPCA/pca_data neighbors_method: neighbors_method k: k out: [find_neighbors] clusterData: run: tools/8_clusterData.cwl in: script: clusterDataR dataFile: findNeighbors/find_neighbors out: [cluster_data] runUMAP: run: tools/9_runUMAP.cwl in: script: runUmapR dataFile: findNeighbors/find_neighbors out: [run_umap_data, run_umap_data_plot] runTSNE: run: tools/10_runTSNE.cwl in: script: runTSNER dataFile: runUMAP/run_umap_data out: [run_tsne_data] findAllMarkers: run: tools/11_findMarkers.cwl in: script: find_markersR dataFile: runTSNE/run_tsne_data out: [find_markers]