generated from opensafely/sro-template
/
project.yaml
51 lines (44 loc) · 1.65 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
version: '3.0'
expectations:
population_size: 10000
actions:
generate_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/cohorts --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/cohorts/input.csv.gz
counts:
run: r:latest analysis/counts.r
needs: [generate_cohort]
outputs:
moderately_sensitive:
death_count: output/tables/death_count.csv
imd_table: output/tables/imd_count.csv
age_sex_table: output/tables/age_sex_count.csv
age_table: output/tables/age_count.csv
ethnicity_table: output/tables/ethnic_group.csv
plots:
run: r:latest analysis/plots.R
needs: [counts]
outputs:
moderately_sensitive:
figure1: output/plots/Cause_of_Death_count.svg
figure2: output/plots/imd_count.svg
figure3: output/plots/age_sex_count.svg
figure4: output/plots/age_count.svg
figure5: output/plots/sex_count.svg
figure6: output/plots/Cause_of_Death_count_eng.svg
figure7: output/plots/age_sex_count_eng.svg
figure8: output/plots/age_count_eng.svg
figure9: output/plots/sex_count_eng.svg
figure10: output/plots/ethnicity_count_eng.svg
figure11: output/plots/ethnicity_count.svg
figure12: output/plots/ethnicity16_count_eng.svg
figure13: output/plots/ethnicity16_count.svg
calculate_tpp_coverage:
run: r:latest analysis/calculate_tpp_coverage.R
needs: [generate_cohort]
outputs:
moderately_sensitive:
region_table: output/tables/tpp_pop_all.csv
region_map: output/plots/tpp_coverage_map.svg