-
Notifications
You must be signed in to change notification settings - Fork 1
/
project.yaml
129 lines (115 loc) · 7.07 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
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
PNV_OS_NC_counts.csv: output/PNV_OS_NC_counts.csv
PWV_OS_NC_counts.csv: output/PWV_OS_NC_counts.csv
PNV_OS_C_counts.csv: output/PNV_OS_C_counts.csv
PWV_OS_C_counts.csv: output/PWV_OS_C_counts.csv