generated from opensafely/research-template
-
Notifications
You must be signed in to change notification settings - Fork 6
/
project.yaml
96 lines (83 loc) · 4.69 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
version: '3.0'
expectations:
population_size: 100000
# dummy population size must be at least 50000 to ensure the STP analysis can run successfully
actions:
generate_delivery_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_delivery.csv.gz
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
needs: [generate_delivery_cohort]
outputs:
moderately_sensitive:
notebook: output/population_characteristics.html
### first, second, third/booster doses
figures: interim-outputs/figures/*
tables: interim-outputs/tables/*
fig_csvs_1: output/machine_readable_outputs/figure_csvs/*ethnicity*.csv
fig_csvs_2: output/machine_readable_outputs/figure_csvs/*imd*.csv
fig_csvs_3: output/machine_readable_outputs/figure_csvs/*psychosis*.csv
fig_csvs_4: output/machine_readable_outputs/figure_csvs/*LD_*.csv
fig_csvs_5: output/machine_readable_outputs/figure_csvs/*eligible*.csv
text: interim-outputs/text/*
generate_simple_report:
run: jupyter:latest env IMAGE_FORMAT=png jupyter nbconvert /workspace/notebooks/opensafely_vaccine_report_overall.ipynb --execute --to html --template basic --output=/workspace/output/opensafely_vaccine_report_overall_simple.html --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_delivery_cohort, generate_notebook]
outputs:
moderately_sensitive:
notebook: output/opensafely_vaccine_report_overall_simple.html
csvs: output/machine_readable_outputs/table_csvs/*
generate_report_second_doses:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/second_doses.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_notebook]
outputs:
moderately_sensitive:
notebook: output/second_doses.html
tables: output/machine_readable_outputs/second_doses/*.csv
generate_report_third_doses:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/booster-third-doses.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_notebook]
outputs:
moderately_sensitive:
notebook: output/booster-third-doses.html
tables: output/machine_readable_outputs/third_doses/*.csv
generate_u16_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery_u16 --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_delivery_u16.csv.gz
generate_u16_notebook:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics_u16.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
needs: [generate_u16_cohort]
outputs:
moderately_sensitive:
notebook: output/population_characteristics_u16.html
figures: interim-outputs/u16/figures/*
tables: interim-outputs/u16/tables/*
fig_csvs: output/machine_readable_outputs/figure_csvs/*_u16*.csv
text: interim-outputs/u16/text/*
generate_u16_simple_report:
run: jupyter:latest env IMAGE_FORMAT=png jupyter nbconvert /workspace/notebooks/first_dose_u16.ipynb --execute --to html --template basic --output=/workspace/output/first_dose_u16.html --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_u16_cohort, generate_u16_notebook]
outputs:
moderately_sensitive:
notebook: output/first_dose_u16.html
csvs: output/machine_readable_outputs/table_csvs/*_u16*.csv
generate_u16_report_second_doses:
run: jupyter:latest jupyter nbconvert /workspace/notebooks/second_doses_u16.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs: [generate_u16_notebook]
outputs:
moderately_sensitive:
notebook: output/second_doses_u16.html
tables: output/machine_readable_outputs/second_doses/*_u16*.csv
generate_u16_publication_objects:
run: r:latest analysis/generate_u16_publication_objects.R
needs: [generate_u16_notebook]
outputs:
moderately_sensitive:
table: interim-outputs/u16/tables/u16_publication_table.csv
figure_option1: interim-outputs/u16/figures/u16_publication_figure.png
figure_option2: interim-outputs/u16/figures/u16_publication_figure_labels.png