generated from opensafely/research-template
-
Notifications
You must be signed in to change notification settings - Fork 0
/
project.yaml
135 lines (115 loc) · 4.55 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
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
################################################################################
#
# Description: This script defines the project pipeline - it specifys the
# execution orders for all the code in this repo using a series of
# actions.
#
# Author(s): M Green
# Date last updated: 07/08/2023
#
################################################################################
version: '3.0'
expectations:
population_size: 1000
actions:
# Extract isaric data (ehrQL) ----
extract_first_isaric_admission:
run: >
ehrql:v0 generate-dataset analysis/dataset_definition_isaric.py
--output 'output/admissions/isaric_admission1.csv.gz'
outputs:
highly_sensitive:
csv: output/admissions/isaric_admission1.csv.gz
# Extract sus data (ehrQL)----
extract_first_sus_admission_methodA_ehrQL:
run: >
ehrql:v0
generate-dataset analysis/dataset_definition_sus.py
--output output/admissions/sus_methodA_admission1_ehrQL.csv.gz
--
--admission_method A
outputs:
highly_sensitive:
cohort: output/admissions/sus_methodA_admission1_ehrQL.csv.gz
extract_first_sus_admission_methodB_ehrQL:
run: >
ehrql:v0
generate-dataset analysis/dataset_definition_sus.py
--output output/admissions/sus_methodB_admission1_ehrQL.csv.gz
--
--admission_method B
outputs:
highly_sensitive:
cohort: output/admissions/sus_methodB_admission1_ehrQL.csv.gz
extract_first_sus_admission_methodC_ehrQL:
run: >
ehrql:v0
generate-dataset analysis/dataset_definition_sus.py
--output output/admissions/sus_methodC_admission1_ehrQL.csv.gz
--
--admission_method C
outputs:
highly_sensitive:
cohort: output/admissions/sus_methodC_admission1_ehrQL.csv.gz
# Extract sus data (cohortextractor)----
extract_sus_methodA_admission1_cohortextractor:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_sus
--output-file output/admissions/sus_methodA_admission1_cohortextractor.csv.gz
--param admission_number=1
--param admission_method=A
outputs:
highly_sensitive:
csv: output/admissions/sus_methodA_admission1_cohortextractor.csv.gz
extract_sus_methodB_admission1_cohortextractor:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_sus
--output-file output/admissions/sus_methodB_admission1_cohortextractor.csv.gz
--param admission_number=1
--param admission_method=B
outputs:
highly_sensitive:
csv: output/admissions/sus_methodB_admission1_cohortextractor.csv.gz
extract_sus_methodC_admission1_cohortextractor:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_sus
--output-file output/admissions/sus_methodC_admission1_cohortextractor.csv.gz
--param admission_number=1
--param admission_method=C
outputs:
highly_sensitive:
csv: output/admissions/sus_methodC_admission1_cohortextractor.csv.gz
# Data properties ----
data_properties:
run: >
r:latest
analysis/rcode/descriptive/data_properties.R
output/admissions/isaric_admission1.csv.gz
output/admissions/sus_methodA_admission1_cohortextractor.csv.gz
output/admissions/sus_methodA_admission1_ehrQL.csv.gz
output/data_properties
needs: [extract_first_isaric_admission, extract_sus_methodA_admission1_cohortextractor, extract_first_sus_admission_methodA_ehrQL]
outputs:
moderately_sensitive:
txt1: output/data_properties/*.txt
# ehrQL vs cohortextractor ----
ehrQL_vs_cohortextractor_comparison:
run: >
r:latest
analysis/rcode/translation/ehrQL_vs_cohortextractor_comparison.R
needs: [extract_first_sus_admission_methodA_ehrQL, extract_first_sus_admission_methodB_ehrQL, extract_first_sus_admission_methodC_ehrQL, extract_sus_methodA_admission1_cohortextractor, extract_sus_methodB_admission1_cohortextractor, extract_sus_methodC_admission1_cohortextractor]
outputs:
moderately_sensitive:
csv: output/translation/ehrQL_vs_cohortextractor_comparison.csv
# Data processing ----
data_process:
run: >
r:latest
analysis/rcode/process/process_data.R
needs: [extract_first_isaric_admission, extract_first_sus_admission_methodA_ehrQL, extract_first_sus_admission_methodB_ehrQL, extract_first_sus_admission_methodC_ehrQL]
outputs:
highly_sensitive:
rds: output/admissions/processed_*.rds