-
Notifications
You must be signed in to change notification settings - Fork 1
/
project.yaml
125 lines (111 loc) · 6.82 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
version: '3.0'
expectations:
population_size: 1000
actions:
# generate_study_population:
# run: cohortextractor:latest generate_cohort --study-definition study_definition
# outputs:
# highly_sensitive:
# cohort: output/input.csv
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2
outputs:
highly_sensitive:
cohort: output/input_2.csv
# generate_study_population_cohort_check:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
# outputs:
# highly_sensitive:
# cohort: output/input_*.csv
# generate_study_population_codelist_check:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_codelist_check
# outputs:
# highly_sensitive:
# cohort: output/input_*.csv
# generate_study_population_vacc_check_anyTest:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_vacc_check_anyTest
# outputs:
# highly_sensitive:
# cohort: output/input_vacc_check.csv
# generate_study_population_vacc_check_posTest:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_vacc_check_posTest
# outputs:
# highly_sensitive:
# cohort: output/input_vacc_check_posTest.csv
# check_cohort:
# run: r:latest analysis/check_cohort.R
# needs: [generate_study_population_cohort_check]
# outputs:
# moderately_sensitive:
# cohort: output/check_cohort.csv
# check_codelist:
# run: r:latest analysis/check_codelist.R
# needs: [generate_study_population_codelist_check]
# outputs:
# moderately_sensitive:
# cohort: output/check_codelist.csv
# 4wk_onboarding:
# run: r:latest analysis/report.R
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# n_patients: output/count_patients.csv
##cohort1: output/plot_postOp_mortality_30day.png
# subtable_table1_ageGroup: output/table1_ageGroup.csv
# subtable_table1_Sex: output/table1_Sex.csv
# subtable_table1_30dayMortality: output/table1_postOp_mortality_30day.csv
# table1_df_4wk: output/table1_4wk_onboarding.csv
##table1_kable_4wk: output/Table1_4wk_onboarding.png
# subtable_table1_ageGroup_3mths: output/table1_ageGroup_3mths.csv
# subtable_table1_Sex_3mths: output/table1_Sex_3mths.csv
# subtable_table1_30dayMortality_3mths: output/table1_postOp_mortality_30day_3mths.csv
# table1_df_4wk_3mths: output/table1_4wk_onboarding_3mths.csv
##table1_kable_4wk_3mths: output/Table1_4wk_onboarding_3mths.png
# subtable_table1_ageGroup_6mths: output/table1_ageGroup_6mths.csv
# subtable_table1_Sex_6mths: output/table1_Sex_6mths.csv
# subtable_table1_30dayMortality_6mths: output/table1_postOp_mortality_30day_6mths.csv
# table1_df_4wk_6mths: output/table1_4wk_onboarding_6mths.csv
##table1_kable_4wk_6mths: output/Table1_4wk_onboarding_6mths.png
# tableVacc_30dayMortality: output/tableVacc_postOp_mortality_30day.csv
# tableVacc_df: output/table_Vaccination_status.csv
##tableVacc_kable: output/TableVacc.png
# tableVacc_30dayMortality_3mths: output/tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_df_3mths: output/table_Vaccination_status_3mths.csv
##tableVacc_kable_3mths: output/TableVacc_3mths.png
# tableVacc_30dayMortality_6mths: output/tableVacc_postOp_mortality_30day_6mths.csv
# tableVacc_df_6mths: output/table_Vaccination_status_6mths.csv
##tableVacc_kable_6mths: output/TableVacc_6mths.png
# vacc_definition_check_anyTest:
# run: r:latest analysis/vacc_check.R
# needs: [generate_study_population_vacc_check_anyTest]
# outputs:
# moderately_sensitive:
# tableVacc_30dayMortality_3mths_SNOMED: output/SNOMED_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_TPP: output/TPP_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_AlwynSNOMED: output/AlwynSNOMED_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_AlwynTPP: output/AlwynTPP_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_df_check_3mths_SNOMED: output/SNOMED_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_TPP: output/TPP_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_AlwynSNOMED: output/AlwynSNOMED_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_AlwynTPP: output/AlwynTPP_table_Vaccination_status_3mths.csv
# vacc_definition_check_posTest:
# run: r:latest analysis/vacc_check.R
# needs: [generate_study_population_vacc_check_posTest]
# outputs:
# moderately_sensitive:
# tableVacc_30dayMortality_3mths_SNOMED: output/SNOMED_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_TPP: output/TPP_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_AlwynSNOMED: output/AlwynSNOMED_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_AlwynTPP: output/AlwynTPP_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_df_check_3mths_SNOMED: output/SNOMED_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_TPP: output/TPP_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_AlwynSNOMED: output/AlwynSNOMED_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_AlwynTPP: output/AlwynTPP_table_Vaccination_status_3mths.csv
COVIDSurg_compare:
run: r:latest analysis/Make_table_COVIDSurg_compare.R
needs: [generate_study_population_2]
outputs:
moderately_sensitive:
table_counts: output/table_Count_of_patients_in_each_cohort_in_each_era_across_all_intervals.csv
table_mortality_intervals: output/table_30day_post-op_mortality_in_each_era_across_all_intervals.csv
table_mortality_totals: output/table_30day_post-op_mortality_for_each_cohort_in_each_era.csv