generated from opensafely/research-template
/
project.yaml
318 lines (285 loc) · 9.28 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
hcw_extract:
run: cohortextractor:latest generate_cohort --study-definition study_definition_hcw
--output-format feather
outputs:
highly_sensitive:
cohort: output/input_hcw.feather
hcw_process:
run: r:latest analysis/hcw/process.R
needs:
- hcw_extract
outputs:
highly_sensitive:
data: output/data/hcw_data_processed.rds
datavax: output/data/hcw_data_vax.rds
hcw_properties:
run: r:latest analysis/process/data_properties.R output/data/hcw_data_processed.rds
output/data_properties
needs:
- hcw_process
outputs:
moderately_sensitive:
cohort: output/data_properties/hcw_data_processed*.txt
hcw_descr:
run: r:latest analysis/hcw/descr.R
needs:
- hcw_process
outputs:
moderately_sensitive:
png: output/hcw/*.png
svg: output/hcw/*.svg
html: output/hcw/*.html
csv: output/hcw/*.csv
design:
run: r:latest analysis/process/design.R
outputs:
moderately_sensitive:
metadata: output/data/metadata*
extract:
run: cohortextractor:latest generate_cohort --study-definition study_definition
--output-format feather
outputs:
highly_sensitive:
cohort: output/input.feather
data_process:
run: r:latest analysis/process/data_process.R
needs:
- extract
outputs:
highly_sensitive:
cohort: output/data/data_processed.rds
data_properties:
run: r:latest analysis/process/data_properties.R output/data/data_processed.rds
output/data_properties
needs:
- data_process
outputs:
highly_sensitive:
cohort: output/data_properties/data_processed*.txt
data_selection:
run: r:latest analysis/process/data_selection.R
needs:
- data_process
outputs:
highly_sensitive:
data_allvax: output/data/data_cohort_allvax.rds
data: output/data/data_cohort.rds
moderately_sensitive:
flow: output/data/flowchart.csv
descr_table1:
run: r:latest analysis/descriptive/table1.R
needs:
- design
- data_selection
outputs:
moderately_sensitive:
html: output/descriptive/tables/table1*.html
csv: output/descriptive/tables/table1*.csv
descr_table1_allvax:
run: r:latest analysis/descriptive/table1_allvax.R
needs:
- design
- data_selection
outputs:
moderately_sensitive:
html: output/descriptive/tables/table1_allvax.html
csv: output/descriptive/tables/table1_allvax.csv
descr_irr:
run: r:latest analysis/descriptive/table_irr.R output/data/data_processed.rds
output/data_properties
needs:
- design
- data_selection
outputs:
moderately_sensitive:
html: output/descriptive/tables/table_irr.html
csv: output/descriptive/tables/table_irr.csv
descr_km:
run: r:latest analysis/descriptive/km.R output/data/data_processed.rds output/data_properties
needs:
- design
- data_selection
outputs:
moderately_sensitive:
png: output/descriptive/km/plot_survival*.png
svg: output/descriptive/km/plot_survival*.svg
model_test_timesincevax:
run: r:latest analysis/models/model_cox.R test timesincevax
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/test/timesincevax/data_cox_split.rds
models: output/test/timesincevax/model*.rds
moderately_sensitive:
logs: output/test/timesincevax/log*.txt
glance: output/test/timesincevax/glance*.csv
report_test_timesincevax:
run: r:latest analysis/models/report_cox.R test timesincevax
needs:
- design
- model_test_timesincevax
outputs:
moderately_sensitive:
svg: output/test/timesincevax/forest*.svg
png: output/test/timesincevax/forest*.png
csv: output/test/timesincevax/estimates*.csv
model_test_calendar:
run: r:latest analysis/models/model_cox.R test calendar
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/test/calendar/data_cox_split.rds
models: output/test/calendar/model*.rds
moderately_sensitive:
logs: output/test/calendar/log*.txt
glance: output/test/calendar/glance*.csv
report_test_calendar:
run: r:latest analysis/models/report_cox.R test calendar
needs:
- design
- model_test_calendar
outputs:
moderately_sensitive:
svg: output/test/calendar/forest*.svg
png: output/test/calendar/forest*.png
csv: output/test/calendar/estimates*.csv
model_postest_timesincevax:
run: r:latest analysis/models/model_cox.R postest timesincevax
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/postest/timesincevax/data_cox_split.rds
models: output/postest/timesincevax/model*.rds
moderately_sensitive:
logs: output/postest/timesincevax/log*.txt
glance: output/postest/timesincevax/glance*.csv
report_postest_timesincevax:
run: r:latest analysis/models/report_cox.R postest timesincevax
needs:
- design
- model_postest_timesincevax
outputs:
moderately_sensitive:
svg: output/postest/timesincevax/forest*.svg
png: output/postest/timesincevax/forest*.png
csv: output/postest/timesincevax/estimates*.csv
model_postest_calendar:
run: r:latest analysis/models/model_cox.R postest calendar
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/postest/calendar/data_cox_split.rds
models: output/postest/calendar/model*.rds
moderately_sensitive:
logs: output/postest/calendar/log*.txt
glance: output/postest/calendar/glance*.csv
report_postest_calendar:
run: r:latest analysis/models/report_cox.R postest calendar
needs:
- design
- model_postest_calendar
outputs:
moderately_sensitive:
svg: output/postest/calendar/forest*.svg
png: output/postest/calendar/forest*.png
csv: output/postest/calendar/estimates*.csv
model_emergency_timesincevax:
run: r:latest analysis/models/model_cox.R emergency timesincevax
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/emergency/timesincevax/data_cox_split.rds
models: output/emergency/timesincevax/model*.rds
moderately_sensitive:
logs: output/emergency/timesincevax/log*.txt
glance: output/emergency/timesincevax/glance*.csv
report_emergency_timesincevax:
run: r:latest analysis/models/report_cox.R emergency timesincevax
needs:
- design
- model_emergency_timesincevax
outputs:
moderately_sensitive:
svg: output/emergency/timesincevax/forest*.svg
png: output/emergency/timesincevax/forest*.png
csv: output/emergency/timesincevax/estimates*.csv
model_emergency_calendar:
run: r:latest analysis/models/model_cox.R emergency calendar
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/emergency/calendar/data_cox_split.rds
models: output/emergency/calendar/model*.rds
moderately_sensitive:
logs: output/emergency/calendar/log*.txt
glance: output/emergency/calendar/glance*.csv
report_emergency_calendar:
run: r:latest analysis/models/report_cox.R emergency calendar
needs:
- design
- model_emergency_calendar
outputs:
moderately_sensitive:
svg: output/emergency/calendar/forest*.svg
png: output/emergency/calendar/forest*.png
csv: output/emergency/calendar/estimates*.csv
model_covidadmitted_timesincevax:
run: r:latest analysis/models/model_cox.R covidadmitted timesincevax
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/covidadmitted/timesincevax/data_cox_split.rds
models: output/covidadmitted/timesincevax/model*.rds
moderately_sensitive:
logs: output/covidadmitted/timesincevax/log*.txt
glance: output/covidadmitted/timesincevax/glance*.csv
report_covidadmitted_timesincevax:
run: r:latest analysis/models/report_cox.R covidadmitted timesincevax
needs:
- design
- model_covidadmitted_timesincevax
outputs:
moderately_sensitive:
svg: output/covidadmitted/timesincevax/forest*.svg
png: output/covidadmitted/timesincevax/forest*.png
csv: output/covidadmitted/timesincevax/estimates*.csv
model_covidadmitted_calendar:
run: r:latest analysis/models/model_cox.R covidadmitted calendar
needs:
- design
- data_selection
outputs:
highly_sensitive:
data: output/covidadmitted/calendar/data_cox_split.rds
models: output/covidadmitted/calendar/model*.rds
moderately_sensitive:
logs: output/covidadmitted/calendar/log*.txt
glance: output/covidadmitted/calendar/glance*.csv
report_covidadmitted_calendar:
run: r:latest analysis/models/report_cox.R covidadmitted calendar
needs:
- design
- model_covidadmitted_calendar
outputs:
moderately_sensitive:
svg: output/covidadmitted/calendar/forest*.svg
png: output/covidadmitted/calendar/forest*.png
csv: output/covidadmitted/calendar/estimates*.csv