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pipeline.cwl
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pipeline.cwl
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class: Workflow
cwlVersion: v1.0
inputs:
raw_file:
type: File
secondary_analysis_file:
type: File
outputs:
raw_anndata_file:
type: File
outputSource: plaintext_to_old_anndata/raw_anndata_file
secondary_analysis_anndata_file:
type: File
outputSource: plaintext_to_old_anndata/secondary_analysis_anndata_file
steps:
new_anndata_to_plaintext:
run: steps/new_anndata_to_plaintext.cwl
in:
raw_file:
source: raw_file
secondary_analysis_file:
source: secondary_analysis_file
out: [raw_mtx_file, raw_var_file, raw_obs_file, sa_mtx_file, sa_var_file, sa_obs_file]
plaintext_to_old_anndata:
run: steps/plaintext_to_old_anndata.cwl
in:
raw_mtx_file:
source: new_anndata_to_plaintext/raw_mtx_file
raw_var_file:
source: new_anndata_to_plaintext/raw_var_file
raw_obs_file:
source: new_anndata_to_plaintext/raw_obs_file
sa_mtx_file:
source: new_anndata_to_plaintext/sa_mtx_file
sa_var_file:
source: new_anndata_to_plaintext/sa_var_file
sa_obs_file:
source: new_anndata_to_plaintext/sa_obs_file
out: [raw_anndata_file, secondary_analysis_anndata_file]