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pipeline.cwl
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pipeline.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
inputs:
assay:
label: "single-cell/nucleus assay"
type: string
reference:
label: "Reference type to map data to"
type: string
matrix:
label: "h5 matrix containing raw counts"
type: File
secondary-analysis-matrix:
label: "h5 matrix to save annotations to"
type: File
outputs:
azimuth_annotated_h5ad:
outputSource: write_metadata/annotated_matrix
type: File
label: "final secondary analysis matrix with all labels and metadata"
steps:
expr_h5ad_adjust:
run: steps/expr-h5ad-adjust.cwl
in:
assay:
source: assay
matrix:
source: matrix
out:
- matrix_adj
extract_rna_secondary_matrix:
run: steps/extract-rna-secondary-matrix.cwl
in:
secondary_analysis_matrix:
source: secondary-analysis-matrix
out:
- rna_secondary_analysis_matrix
azimuth:
run: steps/azimuth-annotate.cwl
in:
reference:
source: reference
matrix:
source: expr_h5ad_adjust/matrix_adj
secondary_analysis_matrix:
source: extract_rna_secondary_matrix/rna_secondary_analysis_matrix
out:
- annotated_matrix
- version_metadata
- annotations_csv
write_metadata:
run: steps/write-metadata.cwl
in:
orig_secondary_analysis_matrix:
source: secondary-analysis-matrix
secondary_analysis_matrix:
source: azimuth/annotated_matrix
annotations_csv:
source: azimuth/annotations_csv
version_metadata:
source: azimuth/version_metadata
out:
- annotated_matrix