generated from opensafely/research-template
/
project.yaml
77 lines (65 loc) · 2.48 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
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
version: '3.0'
expectations:
population_size: 100000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input.csv.gz
data_process:
run: r:latest analysis/data_process.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data1: output/data/data_processed_day0.rds
data2: output/data/data_processed_day5.rds
data_properties_process_day0:
run: r:latest analysis/data_properties.R output/data/data_processed_day0.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
txt1: output/data_properties/data_processed_day0_skim.txt
txt2: output/data_properties/data_processed_day0_coltypes.txt
txt3: output/data_properties/data_processed_day0_tabulate.txt
data_properties_process_day5:
run: r:latest analysis/data_properties.R output/data/data_processed_day5.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
txt1: output/data_properties/data_processed_day5_skim.txt
txt2: output/data_properties/data_processed_day5_coltypes.txt
txt3: output/data_properties/data_processed_day5_tabulate.txt
crosstab_trt_outcomes:
run: r:latest analysis/crosstab_trt_outcomes.R
needs: [data_process]
outputs:
moderately_sensitive:
csvsday5: output/data_properties/day5_*.csv
csvsday0: output/data_properties/day0_*.csv
table_1_day5:
run: r:latest analysis/table_1.R day5
needs: [data_process]
outputs:
highly_sensitive:
data: output/tables/table1_redacted_day5.rds
moderately_sensitive:
table: output/tables/table1_redacted_day5.html
cox_day5:
run: r:latest analysis/cox_models.R day5
needs: [data_process]
outputs:
highly_sensitive:
data: output/tables/cox_models_day5.rds
moderately_sensitive:
figure1: output/figs/*_overlap_plot_day5_before_restriction.png
figure2: output/figs/*_overlap_plot_day5_after_restriction.png
figure3: output/figs/*_cumInc_day5.png
table1: output/tables/cox_models_day5.csv
table2: output/tables/log_cox_models_day5.csv
trt_pat_day5:
run: r:latest analysis/treatment_distributions.R day5
needs: [data_process]
outputs:
moderately_sensitive:
figure: output/figs/day5_treatment_pattern.png