/
project.yaml
107 lines (95 loc) · 4.18 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
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population_ethnicity_01H08E5TR9JRWX6D1BK8PWV54X:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity
--output-dir output/01H08E5TR9JRWX6D1BK8PWV54X --output-format=feather
outputs:
highly_sensitive:
cohort: output/01H08E5TR9JRWX6D1BK8PWV54X/input_ethnicity.feather
generate_study_population_weekly_01H08E5TR9JRWX6D1BK8PWV54X:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--param codelist_1_frequency="weekly"
--param breakdowns=""
--index-date_range="2023-04-24 to 2023-04-24 by week"
--output-dir=output/01H08E5TR9JRWX6D1BK8PWV54X
--output-format=feather
--output-file=output/01H08E5TR9JRWX6D1BK8PWV54X/input_weekly_2023-04-24.feather
outputs:
highly_sensitive:
cohort: output/01H08E5TR9JRWX6D1BK8PWV54X/input_weekly_2023-04-24.feather
generate_study_population_01H08E5TR9JRWX6D1BK8PWV54X:
run: cohortextractor:latest generate_cohort
--study-definition study_definition
--index-date-range="2019-09-01 to 2023-04-30 by month"
--output-dir=output/01H08E5TR9JRWX6D1BK8PWV54X
--output-format=feather
outputs:
highly_sensitive:
cohort: output/01H08E5TR9JRWX6D1BK8PWV54X/input_*.feather
join_cohorts_01H08E5TR9JRWX6D1BK8PWV54X:
run: >
cohort-joiner:v0.0.38
--lhs output/01H08E5TR9JRWX6D1BK8PWV54X/input_20*.feather
--rhs output/01H08E5TR9JRWX6D1BK8PWV54X/input_ethnicity.feather
--output-dir output/01H08E5TR9JRWX6D1BK8PWV54X/joined
needs: [generate_study_population_01H08E5TR9JRWX6D1BK8PWV54X, generate_study_population_ethnicity_01H08E5TR9JRWX6D1BK8PWV54X]
outputs:
highly_sensitive:
cohort: output/01H08E5TR9JRWX6D1BK8PWV54X/joined/input_20*.feather
generate_measures_01H08E5TR9JRWX6D1BK8PWV54X:
run: >
python:latest -m analysis.measures
--breakdowns=sex
--breakdowns=age
--breakdowns=ethnicity
--breakdowns=imd
--breakdowns=region
--input-dir="output/01H08E5TR9JRWX6D1BK8PWV54X/joined"
needs: [join_cohorts_01H08E5TR9JRWX6D1BK8PWV54X]
outputs:
moderately_sensitive:
measure: output/01H08E5TR9JRWX6D1BK8PWV54X/joined/measure_all.csv
decile_measure: output/01H08E5TR9JRWX6D1BK8PWV54X/joined/measure_practice_rate_deciles.csv
top_5_table_01H08E5TR9JRWX6D1BK8PWV54X:
run: >
python:latest python analysis/top_5.py
--codelist-1-path="interactive_codelists/codelist_1.csv"
--codelist-2-path="interactive_codelists/codelist_2.csv"
--output-dir="output/01H08E5TR9JRWX6D1BK8PWV54X"
needs: [generate_measures_01H08E5TR9JRWX6D1BK8PWV54X]
outputs:
moderately_sensitive:
tables: output/01H08E5TR9JRWX6D1BK8PWV54X/joined/top_5*.csv
plot_measure_01H08E5TR9JRWX6D1BK8PWV54X:
run: >
python:latest python analysis/plot_measures.py
--breakdowns=sex
--breakdowns=age
--breakdowns=ethnicity
--breakdowns=imd
--breakdowns=region
--output-dir output/01H08E5TR9JRWX6D1BK8PWV54X
needs: [generate_measures_01H08E5TR9JRWX6D1BK8PWV54X]
outputs:
moderately_sensitive:
measure: output/01H08E5TR9JRWX6D1BK8PWV54X/plot_measure*.png
deciles: output/01H08E5TR9JRWX6D1BK8PWV54X/deciles_chart.png
event_counts_01H08E5TR9JRWX6D1BK8PWV54X:
run: >
python:latest -m analysis.event_counts --input-dir="output/01H08E5TR9JRWX6D1BK8PWV54X" --output-dir="output/01H08E5TR9JRWX6D1BK8PWV54X"
needs: [join_cohorts_01H08E5TR9JRWX6D1BK8PWV54X, generate_study_population_weekly_01H08E5TR9JRWX6D1BK8PWV54X]
outputs:
moderately_sensitive:
measure: output/01H08E5TR9JRWX6D1BK8PWV54X/event_counts.json
generate_report_01H08E5TR9JRWX6D1BK8PWV54X:
run: >
python:latest python analysis/render_report.py
--output-dir="output/01H08E5TR9JRWX6D1BK8PWV54X"
needs: [event_counts_01H08E5TR9JRWX6D1BK8PWV54X, top_5_table_01H08E5TR9JRWX6D1BK8PWV54X, plot_measure_01H08E5TR9JRWX6D1BK8PWV54X]
outputs:
moderately_sensitive:
notebook: output/01H08E5TR9JRWX6D1BK8PWV54X/report.html