generated from opensafely/research-template
/
project.yaml
47 lines (35 loc) · 1.08 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
######################################
# This script defines the project pipeline - it specifys the execution orders for all the code in this
# repo using a series of actions.
######################################
version: '3.0'
expectations:
population_size: 100000
actions:
# Extract data ----
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/data
outputs:
highly_sensitive:
cohort: output/data/input.csv
# Process data ----
data_process:
run: r:latest analysis/data_process.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data: output/data/data_all.rds
# Table 1 ----
table_1:
run: r:latest analysis/table_1.R
needs: [data_process]
outputs:
moderately_sensitive:
table: output/tables/table1.html
# Table 2 ----
table_2:
run: r:latest analysis/table_2.R
needs: [data_process]
outputs:
moderately_sensitive:
table: output/tables/table2.html