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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
# Extract data
generate_study_population_wave4:
run: >
cohortextractor:latest generate_cohort
--study-definition study_definition_wave4
--skip-existing
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/input_wave4.csv.gz
# Process data
process_data_wave4:
run: r:latest analysis/data_process.R wave4
needs: [generate_study_population_wave4]
outputs:
highly_sensitive:
rds: output/processed/input_wave4.rds
# Skim data
skim_data_wave4:
run: r:latest analysis/data_skim.R output/processed/input_wave4.rds output/data_properties
needs: [process_data_wave4]
outputs:
moderately_sensitive:
txt1: output/data_properties/input_wave4_skim.txt
txt2: output/data_properties/input_wave4_coltypes.txt
txt3: output/data_properties/input_wave4_tabulate.txt
# Filter data
filter_data_wave4:
run: r:latest analysis/data_selection.R wave4
needs: [process_data_wave4]
outputs:
highly_sensitive:
rds: output/filtered/input_wave4.rds
moderately_sensitive:
csv: output/flowchart/flowchart_wave4.csv
# Table 1
table_1_wave4_all:
run: r:latest analysis/table_1.R wave4 all
needs: [filter_data_wave4]
outputs:
highly_sensitive:
data: output/table_1/table_1_wave4_all.rds
moderately_sensitive:
table: output/table_1/table_1_wave4_all.html
csv: output/table_1/table_1_wave4_all.csv
table_1_wave4_transplant:
run: r:latest analysis/table_1.R wave4 transplant
needs: [filter_data_wave4]
outputs:
highly_sensitive:
data: output/table_1/table_1_wave4_transplant.rds
moderately_sensitive:
table: output/table_1/table_1_wave4_transplant.html
csv: output/table_1/table_1_wave4_transplant.csv
table_1_wave4_haem_cancer:
run: r:latest analysis/table_1.R wave4 haem_cancer
needs: [filter_data_wave4]
outputs:
highly_sensitive:
data: output/table_1/table_1_wave4_haem_cancer.rds
moderately_sensitive:
table: output/table_1/table_1_wave4_haem_cancer.html
csv: output/table_1/table_1_wave4_haem_cancer.csv
table_1_wave4_imm:
run: r:latest analysis/table_1.R wave4 imm
needs: [filter_data_wave4]
outputs:
highly_sensitive:
data: output/table_1/table_1_wave4_imm.rds
moderately_sensitive:
table: output/table_1/table_1_wave4_imm.html
csv: output/table_1/table_1_wave4_imm.csv
table_1_wave4_imd:
run: r:latest analysis/table_1.R wave4 imd
needs: [filter_data_wave4]
outputs:
highly_sensitive:
data: output/table_1/table_1_wave4_imd.rds
moderately_sensitive:
table: output/table_1/table_1_wave4_imd.html
csv: output/table_1/table_1_wave4_imd.csv
table_1_wave4_radio_chemo:
run: r:latest analysis/table_1.R wave4 radio_chemo
needs: [filter_data_wave4]
outputs:
highly_sensitive:
data: output/table_1/table_1_wave4_radio_chemo.rds
moderately_sensitive:
table: output/table_1/table_1_wave4_radio_chemo.html
csv: output/table_1/table_1_wave4_radio_chemo.csv