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dockstoreyml_test.yml
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dockstoreyml_test.yml
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version: 1.2
workflows:
- name: scsorter_run
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/scsorter_run.wdl
testParameterFiles:
- ./input_jsons/scsorter_run_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: multisample_seurat
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/multisample_seurat.wdl
testParameterFiles:
- ./input_jsons/multisample_seurat_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: linear_chain_adddoublets_seurat
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/linear_chain_adddoublets_seurat.wdl
testParameterFiles:
- ./input_jsons/linear_chain_adddoublets_seurat_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: singleR_immune_nonimmune_pipeline
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/singleR_immune_nonimmune_pipeline.wdl
testParameterFiles:
- ./input_jsons/singleR_immune_nonimmune_pipeline_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: plot_qc
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/plot_qc.wdl
testParameterFiles:
- ./input_jsons/plot_qc_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: SingleR_singleref
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/SingleR_singleref.wdl
testParameterFiles:
- ./input_jsons/SingleR_singleref_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: add_doubletinfo
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/add_doubletinfo.wdl
testParameterFiles:
- ./input_jsons/add_doubletinfo_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: clustering_n_pca_simple
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/clustering_n_pca_simple.wdl
testParameterFiles:
- ./input_jsons/clustering_n_pca_simple_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: rpca_integration
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/rpca_integration.wdl
testParameterFiles:
- ./input_jsons/rpca_integration_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: htmap_degs
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/htmap_degs.wdl
testParameterFiles:
- ./input_jsons/htmap_degs_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: add_cellid_results_to_seurat
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/add_cellid_results_to_seurat.wdl
testParameterFiles:
- ./input_jsons/add_cellid_results_to_seurat_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: Doublet_calling
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/Doublet_calling.wdl
testParameterFiles:
- ./input_jsons/Doublet_calling_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: make_gene_featplots
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/make_gene_featplots.wdl
testParameterFiles:
- ./input_jsons/make_gene_featplots_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: LinearChain_htmapdegs
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/LinearChain_htmapdegs.wdl
testParameterFiles:
- ./input_jsons/LinearChain_htmapdegs_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: single_sample_seurat
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/single_sample_seurat.wdl
testParameterFiles:
- ./input_jsons/single_sample_seurat_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: subset_renormalize_recluster
subclass: WDL
publish: true
primaryDescriptorPath: ./tasks/subset_renormalize_recluster.wdl
testParameterFiles:
- ./input_jsons/subset_renormalize_recluster_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: recluster_renorm_rerun_singleR
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/recluster_renorm_rerun_singleR.wdl
testParameterFiles:
- ./input_jsons/recluster_renorm_rerun_singleR_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: scatter_gather_singleR
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/scatter_gather_singleR.wdl
testParameterFiles:
- ./input_jsons/scatter_gather_singleR_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: single_sample_filtering_nd_doublets
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/single_sample_filtering_nd_doublets.wdl
testParameterFiles:
- ./input_jsons/single_sample_filtering_nd_doublets_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: scatter_deg
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/scatter_deg.wdl
testParameterFiles:
- ./input_jsons/scatter_deg_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: scatter_gather_Doubletcall_multisample
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/scatter_gather_Doubletcall_multisample.wdl
testParameterFiles:
- ./input_jsons/scatter_gather_Doubletcall_multisample_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: seurat_counts_to_anndata
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/seurat_counts_to_anndata.wdl
testParameterFiles:
- ./input_jsons/seurat_counts_to_anndata_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: scatter_gather_scsorter
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/scatter_gather_scsorter.wdl
testParameterFiles:
- ./input_jsons/scatter_gather_scsorter_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: single_sample_filtering_n_clustering
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/single_sample_filtering_n_clustering.wdl
testParameterFiles:
- ./input_jsons/single_sample_filtering_n_clustering_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: scatter_gather_doublet_singlesample
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/scatter_gather_doublet_singlesample.wdl
testParameterFiles:
- ./input_jsons/scatter_gather_doublet_singlesample_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: scatter_gather_singleR_bysample
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/scatter_gather_singleR_bysample.wdl
testParameterFiles:
- ./input_jsons/scatter_gather_singleR_bysample_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: scatter_rpca
subclass: WDL
publish: true
primaryDescriptorPath: ./subworkflows/scatter_rpca.wdl
testParameterFiles:
- ./input_jsons/scatter_rpca_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: multisample_seurat_doublet_singler
subclass: WDL
publish: true
primaryDescriptorPath: ./pipelines/multisample_seurat_doublet_singler.wdl
testParameterFiles:
- ./input_jsons/multisample_seurat_doublet_singler_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: end_to_end_seurat_singlesample
subclass: WDL
publish: true
primaryDescriptorPath: ./pipelines/end_to_end_seurat_singlesample.wdl
testParameterFiles:
- ./input_jsons/end_to_end_seurat_singlesample_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: end_to_end_multisample
subclass: WDL
publish: true
primaryDescriptorPath: ./pipelines/end_to_end_multisample.wdl
testParameterFiles:
- ./input_jsons/end_to_end_multisample_inputs.json
authors:
- orcid: 0000-0002-1385-2056
- name: seurat_single_sample_nomerging
subclass: WDL
publish: true
primaryDescriptorPath: ./pipelines/seurat_single_sample_nomerging.wdl
testParameterFiles:
- ./input_jsons/seurat_single_sample_nomerging_inputs.json
authors:
- orcid: 0000-0002-1385-2056