generated from opensafely/research-template
/
project.yaml
46 lines (38 loc) · 1.78 KB
/
project.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
version: '3.0'
expectations:
population_size: 10000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-06-01 by month" --output-dir=output/data #--output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_*.csv
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output/data #--output-format=feather
outputs:
highly_sensitive:
cohort: output/data/input_ethnicity.csv
join_ethnicity:
run: python:latest python analysis/join_ethnicity.py
needs: [generate_study_population, generate_study_population_ethnicity]
outputs:
highly_sensitive:
cohort: output/data/input*.csv
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/data
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/data/measure_*.csv
generate_abnormal_nb:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/abnormal_results.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [calculate_measures]
outputs:
moderately_sensitive:
notebook: output/abnormal_results.html
generate_levels_nb:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/hba1c_levels.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [join_ethnicity]
outputs:
moderately_sensitive:
notebook: output/hba1c_levels.html