generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
# Generates study population for CV, mental health outcomes
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures --output-format=csv
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv
# Generates study population for diabetes outcomes
generate_study_population_dm:
run: cohortextractor:latest generate_cohort --study-definition study_definition_dm --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures/dm --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/dm/input_dm_*.csv
# Generates study population for respiratory outcomes
generate_study_population_resp:
run: cohortextractor:latest generate_cohort --study-definition study_definition_resp --index-date-range "2018-03-01 to 2022-01-31 by month" --output-dir=output/measures/resp --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/resp/input_resp_*.csv
# Generates study population for mortality
generate_study_population_mortality:
run: cohortextractor:latest generate_cohort --study-definition study_definition_mortality --index-date-range "2019-02-01 to 2022-01-31 by month" --output-dir=output/measures/mortality --output-format=csv --skip-existing
outputs:
highly_sensitive:
cohort: output/measures/mortality/input_mortality_*.csv
# Generates summary measures for CV and mental health outcomes
calculate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure: output/measures/measure_*.csv
# Generates summary measures for diabetes outcomes
calculate_measures_dm:
run: cohortextractor:latest generate_measures --study-definition study_definition_dm --output-dir=output/measures/dm
needs: [generate_study_population_dm]
outputs:
moderately_sensitive:
measure: output/measures/dm/measure_dm_*.csv
# Generates summary measures for respiratory outcomes
calculate_measures_resp:
run: cohortextractor:latest generate_measures --study-definition study_definition_resp --output-dir=output/measures/resp
needs: [generate_study_population_resp]
outputs:
moderately_sensitive:
measure: output/measures/resp/measure_*.csv
# Generates summary measures for mortality outcomes
calculate_measures_mortality:
run: cohortextractor:latest generate_measures --study-definition study_definition_mortality --output-dir=output/measures/mortality
needs: [generate_study_population_mortality]
outputs:
moderately_sensitive:
measure: output/measures/mortality/measure_*.csv
# Generates graphs for CVD & mental health outcomes
graphs_mh_cvd:
run: stata-mp:latest analysis/graphs_mh_cvd.do
needs: [calculate_measures]
outputs:
moderately_sensitive:
log: logs/graphs_mh_cvd.log
output: output/line_*.eps
highly_sensitive:
output: output/measures/measure_*
# Generates graphs for diabetes outcomes
graphs_dm:
run: stata-mp:latest analysis/graphs_dm.do
needs: [calculate_measures_dm]
outputs:
moderately_sensitive:
log: logs/graphs_dm.log
output: output/line_dm_*.eps
# Generate graphs for respiratory outcomes
graphs_resp:
run: stata-mp:latest analysis/graphs_resp.do
needs: [calculate_measures_resp]
outputs:
moderately_sensitive:
log: logs/graphs_resp.log
output: output/line_resp_*.eps
# Generate graphs for mortality
graphs_mortality:
run: stata-mp:latest analysis/graphs_mortality.do
needs: [calculate_measures_mortality]
outputs:
moderately_sensitive:
log: logs/graphs_mortality.log
output: output/line_mortality_*.eps