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update pbmc10k data set download #244

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May 9, 2023
Merged

update pbmc10k data set download #244

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30 changes: 27 additions & 3 deletions reproducibility/figures/dvc.lock
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Original file line number Diff line number Diff line change
Expand Up @@ -2075,8 +2075,8 @@ stages:
cmd: python fig2/figure_extras.py reports.model_summary.summarize=[pancreas_model2,pbmc68k_model2]
deps:
- path: fig2/figure_extras.py
md5: 25ad6282b2e318fbe29d5babbe3aaf1d
size: 5817
md5: e40ad67e697be6dddb77c73719844a38
size: 6017
- path: models/pancreas_model2/pyrovelocity.pkl
md5: 1eeaa0c042af52c18af112c6c33893c3
size: 65873440
Expand All @@ -2101,7 +2101,7 @@ stages:
vector_field_plot: reports/fig2/fig2_pancreas_vector_field.pdf
outs:
- path: reports/fig2/fig2_pancreas_pbmc_uncertainties_comparison.pdf
md5: f1118c261194af09de9871a696bd097f
md5: 8f99726bf73777508059c78bc1ef0bf1
size: 132845
summarize_pbmc10k_model2:
cmd: python summarize.py reports.model_summary.summarize=[pbmc10k_model2]
Expand Down Expand Up @@ -2184,3 +2184,27 @@ stages:
- path: reports/pbmc10k_model2/volcano.pdf
md5: fd08d4f8cbb3715cdbbae4984f9c544a
size: 21847
data_download_pbmc10k:
cmd: echo "Reference pbmc10k"
deps:
- path: data_download.py
md5: 30f38cc794cbf4caad2675ffd88c2467
size: 3305
params:
config.yaml:
base:
log_level: INFO
data_external.pyrovelocity.pbmc10k:
data_file: pbmc10k.h5ad
dl_root: data/external
dl_path: data/external/pbmc10k.h5ad
rel_path: data/external/pbmc10k.h5ad
url: https://ndownloader.figshare.com/files/pbmc10k
derived:
process_method: load_data
process_args: {}
rel_path: data/processed/pbmc10k_processed.h5ad
outs:
- path: data/external/pbmc10k.h5ad
md5: 3b64b4cd122454610957f5c6086e2eac
size: 592149007
12 changes: 12 additions & 0 deletions reproducibility/figures/dvc.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,18 @@ stages:
- ${data_external.scvelo.pbmc68k.rel_path}:
persist: true

data_download_pbmc10k:
cmd: echo "Reference pbmc10k"
deps:
- data_download.py
params:
- config.yaml:
- base
- data_external.pyrovelocity.pbmc10k
outs:
- ${data_external.pyrovelocity.pbmc10k.rel_path}:
persist: true

data_download_larry:
cmd: python data_download.py data_external.sources=[pyrovelocity] data_external.pyrovelocity.download=[larry]
deps:
Expand Down
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