generated from opensafely/research-template
/
project.yaml
139 lines (119 loc) · 4.75 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-10-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/measures/input_*.csv.gz
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv: output/measures/measure_*.csv
describe_overall_OS:
run: r:latest analysis/plot/overall_ab_boxplot_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
boxplot: output/overallbox_os.jpeg
describe_overall_brit:
run: r:latest analysis/plot/overall_ab_boxplot_brit.R
needs: [generate_measures]
outputs:
moderately_sensitive:
boxplot: output/overallbox_brit.jpeg
describe_overall_brit_os:
run: r:latest analysis/plot/overall_ab_boxplot_brit_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
boxplot: output/overallbox_brit_os.jpeg
describe_ab_type_brit:
run: r:latest analysis/plot/stacked_bar_chart_top_10_abtype_brit.R
needs: [generate_measures]
outputs:
moderately_sensitive:
linechart: output/linechart_abtype_brit.jpeg
barchart: output/barchart_abtype_brit.jpeg
table: output/abtype_top10_bymonth_brit.csv
describe_ab_type_brit_os:
run: r:latest analysis/plot/stacked_bar_chart_top_10_abtype_brit_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
linechart: output/linechart_abtype_brit_os.jpeg
barchart: output/barchart_abtype_brit_os.jpeg
table: output/abtype_top10_bymonth_brit_os.csv
describe_percentile_os:
run: r:latest analysis/plot/overall_ab_prescribing_2575percentile_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/overall_25th_75th_percent_os.jpeg
table: output/pres_number_os.csv
describe_percentile_brit:
run: r:latest analysis/plot/overall_ab_prescribing_2575percentile_brit.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/overall_25th_75th_percent_brit.jpeg
table: output/pres_number_brit.csv
describe_percentile_brit_os:
run: r:latest analysis/plot/overall_ab_prescribing_2575percentile_brit_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/overall_25th_75th_percent_brit_os.jpeg
table: output/pres_number_brit_os.csv
describe_starpu_os:
run: r:latest analysis/plot/starpu_ab_prescribing_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
cohort: output/starpu_line_os.jpeg
boxplot: output/starpu_box_os.jpeg
describe_starpu_brit:
run: r:latest analysis/plot/starpu_ab_prescribing_brit.R
needs: [generate_measures]
outputs:
moderately_sensitive:
cohort: output/starpu_line_brit.jpeg
boxplot: output/starpu_box_brit.jpeg
describe_starpu_brit_os:
run: r:latest analysis/plot/starpu_ab_prescribing_brit_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
cohort: output/starpu_line_brit_os.jpeg
boxplot: output/starpu_box_brit_os.jpeg
describe_b_n_brit:
run: r:latest analysis/plot/broad_narrow_bar_chart_brit.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/broad_narrow_bar_chart_brit.jpeg
describe_b_n_brit_os:
run: r:latest analysis/plot/broad_narrow_bar_chart_brit_os.R
needs: [generate_measures]
outputs:
moderately_sensitive:
percentile: output/broad_narrow_bar_chart_brit_os.jpeg
#generate_notebook_starpu:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
#generate_notebook_starpu:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
# needs: [generate_measures]
# outputs:
# moderately_sensitive:
# notebook: output/starpu.html
# figures: output/*
generate_notebook_starpu_brit_os:
run: jupyter:latest jupyter nbconvert /workspace/analysis/starpu_brit_os.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
needs: [generate_measures]
outputs:
moderately_sensitive:
notebook: output/starpu_brit_os.html
figures: output/*