generated from opensafely/research-template
/
project.yaml
57 lines (43 loc) · 1.86 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
47
48
49
50
51
52
53
54
55
56
57
version: '3.0'
expectations:
population_size: 10000
actions:
generate_study_population_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-09-01 to 2021-10-01 by month" --output-dir=output --output-format=csv
outputs:
highly_sensitive:
cohort: output/input*.csv
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-11-01 to 2021-12-01 by month" --output-dir=output --output-format=csv
outputs:
highly_sensitive:
cohort: output/input_*.csv
generate_dose:
run: python:latest python analysis/calculate_dose.py
needs: [generate_study_population_1, generate_study_population_2]
outputs:
highly_sensitive:
cohort: output/inpu*.csv
#generate_study_population_ethnicity:
#run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=csv
#outputs:
#highly_sensitive:
#cohort: output/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/input*.csv
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
needs: [generate_dose]
outputs:
moderately_sensitive:
measure_csv: output/measure_*.csv
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/report.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_measures]
outputs:
moderately_sensitive:
notebook: output/report.html