generated from opensafely/research-template
/
project.yaml
41 lines (34 loc) · 1.3 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
version: '3.0'
expectations:
population_size: 500
actions:
generate_measure_cohort_1:
# week 45 2020 to 20 2020 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition_measure --index-date-range "2020-11-02 to 2020-12-13 by week"
outputs:
highly_sensitive:
cohort: output/input_*.csv
generate_measure_cohort_2:
# week 51 2020 to 03 2021 inclusive
run: cohortextractor:latest generate_cohort --study-definition study_definition_measure --index-date-range "2020-12-14 to 2021-01-24 by week"
outputs:
highly_sensitive:
cohort: output/input*.csv
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition_measure
needs: [generate_measure_cohort_1, generate_measure_cohort_2]
outputs:
moderately_sensitive:
measure: output/measure_*_rate.csv
standardise_and_plot:
run: python:latest python analysis/time_series_plots.py
needs: [calculate_measures]
outputs:
moderately_sensitive:
tables: output/*_rate.csv
graph: output/time_series_plot.svg
generate_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_cohort
outputs:
highly_sensitive:
cohort: output/input_cohort.csv