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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
# Immunosuppression combinations
imm_comb_wave4:
run: r:latest analysis/imm_comb.R wave4
needs: [filter_data_wave4]
outputs:
moderately_sensitive:
csv1: output/imm_comb/imm_comb_wave4_broad.csv
csv2: output/imm_comb/imm_comb_wave4_narrow.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_Tx:
run: r:latest analysis/table_1.R wave4 Tx
needs: [filter_data_wave4]
outputs:
highly_sensitive:
data: output/table_1/table_1_wave4_Tx.rds
moderately_sensitive:
table: output/table_1/table_1_wave4_Tx.html
csv: output/table_1/table_1_wave4_Tx.csv
table_1_wave4_HC:
run: r:latest analysis/table_1.R wave4 HC
needs: [filter_data_wave4]
outputs:
highly_sensitive:
data: output/table_1/table_1_wave4_HC.rds
moderately_sensitive:
table: output/table_1/table_1_wave4_HC.html
csv: output/table_1/table_1_wave4_HC.csv
table_1_wave4_RC:
run: r:latest analysis/table_1.R wave4 RC
needs: [filter_data_wave4]
outputs:
highly_sensitive:
data: output/table_1/table_1_wave4_RC.rds
moderately_sensitive:
table: output/table_1/table_1_wave4_RC.html
csv: output/table_1/table_1_wave4_RC.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
collate_table_1_wave4:
run: r:latest analysis/collate_table_1.R wave4
needs: [table_1_wave4_all, table_1_wave4_Tx, table_1_wave4_HC, table_1_wave4_RC, table_1_wave4_IMM, table_1_wave4_IMD]
outputs:
moderately_sensitive:
csv: output/table_1/table_1_wave4_collated.csv
# Table - incidence rates
calc_ir_hr_wave4_Tx:
run: r:latest analysis/calc_ir_hr.R wave4 Tx
needs: [filter_data_wave4]
outputs:
moderately_sensitive:
csv1: output/table_ir_hr/table_ir_hr_wave4_Tx.csv
csv2: output/table_ir_hr/table_ir_hr_wave4_Tx_simple.csv
calc_ir_hr_wave4_HC:
run: r:latest analysis/calc_ir_hr.R wave4 HC
needs: [filter_data_wave4]
outputs:
moderately_sensitive:
csv1: output/table_ir_hr/table_ir_hr_wave4_HC.csv
csv2: output/table_ir_hr/table_ir_hr_wave4_HC_simple.csv
calc_ir_hr_wave4_RC:
run: r:latest analysis/calc_ir_hr.R wave4 RC
needs: [filter_data_wave4]
outputs:
moderately_sensitive:
csv1: output/table_ir_hr/table_ir_hr_wave4_RC.csv
csv2: output/table_ir_hr/table_ir_hr_wave4_RC_simple.csv
calc_ir_hr_wave4_IMM:
run: r:latest analysis/calc_ir_hr.R wave4 IMM
needs: [filter_data_wave4]
outputs:
moderately_sensitive:
csv1: output/table_ir_hr/table_ir_hr_wave4_IMM.csv
csv2: output/table_ir_hr/table_ir_hr_wave4_IMM_simple.csv
calc_ir_hr_wave4_IMD:
run: r:latest analysis/calc_ir_hr.R wave4 IMD
needs: [filter_data_wave4]
outputs:
moderately_sensitive:
csv1: output/table_ir_hr/table_ir_hr_wave4_IMD.csv
csv2: output/table_ir_hr/table_ir_hr_wave4_IMD_simple.csv