generated from opensafely/research-template
-
Notifications
You must be signed in to change notification settings - Fork 0
/
project.yaml
60 lines (51 loc) · 1.77 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
58
59
60
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
generate_study_population_pbc:
run: cohortextractor:latest generate_cohort --study-definition study_definition_pbc
outputs:
highly_sensitive:
cohort: output/input_pbc.csv
feasibility:
run: stata-mp:latest analysis/feasibility.do
needs: [generate_study_population, generate_study_population_pbc]
outputs:
moderately_sensitive:
log: logs/feasibility.log
table: output/tables/udca*.csv
#table_oba: output/tables/oba*.csv
extract_udca:
run: cohortextractor:latest generate_cohort --study-definition study_definition_additional
needs: [generate_study_population_pbc]
outputs:
highly_sensitive:
cohort: output/input_additional.csv
prep_drug_data:
run: stata-mp:latest analysis/101_drug_prep.do
needs: [extract_udca, generate_study_population_pbc]
outputs:
moderately_sensitive:
log: logs/drug_prep.log
highly_sensitive:
drug_data: output/time_varying_udca*.dta
drug_descriptives:
run: stata-mp:latest analysis/102_udca_descriptives.do
needs: [prep_drug_data, generate_study_population_pbc]
outputs:
moderately_sensitive:
log: logs/udca_descriptives.log
summary: output/tables/udca_descriptives.txt
baseline_tables:
run: stata-mp:latest analysis/103_baseline_tables.do
needs: [generate_study_population_pbc]
outputs:
moderately_sensitive:
log: logs/baseline_tables.log
chars: output/tables/baseline*.csv
meds: output/tables/additional*.csv