generated from opensafely/research-template
/
project.yaml
93 lines (79 loc) · 2.83 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
split_codelist:
run: stata-mp:latest analysis/00_trim_snomed_codelist.do
outputs:
highly_sensitive:
data1: codelists/group1.csv
data2: codelists/group2.csv
data3: codelists/group3.csv
data4: codelists/group4.csv
data5: codelists/group5.csv
data6: codelists/group6.csv
data7: codelists/group7.csv
data8: codelists/group8.csv
data9: codelists/group9.csv
data10: codelists/group10.csv
moderately_sensitive:
log: logs/00_trim_snomed_codelist.log
generate_cohort1:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
generate_cohort2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2
outputs:
highly_sensitive:
cohort: output/input_2.csv
generate_cohort3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_3
outputs:
highly_sensitive:
cohort: output/input_3.csv
generate_cohort4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_4
outputs:
highly_sensitive:
cohort: output/input_4.csv
generate_cohort5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_5
outputs:
highly_sensitive:
cohort: output/input_5.csv
generate_cohort6:
run: cohortextractor:latest generate_cohort --study-definition study_definition_6
outputs:
highly_sensitive:
cohort: output/input_6.csv
generate_cohort7:
run: cohortextractor:latest generate_cohort --study-definition study_definition_7
outputs:
highly_sensitive:
cohort: output/input_7.csv
generate_cohort8:
run: cohortextractor:latest generate_cohort --study-definition study_definition_8
outputs:
highly_sensitive:
cohort: output/input_8.csv
generate_cohort9:
run: cohortextractor:latest generate_cohort --study-definition study_definition_9
outputs:
highly_sensitive:
cohort: output/input_9.csv
generate_cohort10:
run: cohortextractor:latest generate_cohort --study-definition study_definition_10
outputs:
highly_sensitive:
cohort: output/input_10.csv
initial_counts:
run: stata-mp:latest analysis/01_describe_snomed_ethnicity.do
needs: [generate_cohort1, generate_cohort2, generate_cohort3, generate_cohort4, generate_cohort5, generate_cohort6, generate_cohort7, generate_cohort8, generate_cohort9, generate_cohort10]
outputs:
highly_sensitive:
data: output/snomed_ethnicity_counts.dta
table: output/snomed_ethnicity_counts.csv
moderately_sensitive:
log: logs/01_describe_snomed_ethnicity.log