Job Request: 2469 cop7auwjkzfhbaj7

State

State is inferred from the related Jobs
Status: succeeded

Config

Backend: tpp
Workspace: post-covid-competing-risks (reviewer-updates)
Creator: johntaz
Force run dependencies?: True
Git Commit Hash: e058078
Requested Actions:
  • run_all

Timings

Created: 1 week ago
Started: 1 week ago
Finished: 6 days, 18 hours ago
Runtime: 46:54:36

Pipeline

version: "3.0"

expectations:
population_size: 20000

actions:
generate_covid_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid
outputs:
highly_sensitive:
cohort: output/input_covid.csv

generate_covid_community_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covid_community
outputs:
highly_sensitive:
cohort: output/input_covid_community.csv

generate_covid_general_population_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_general_population
outputs:
highly_sensitive:
cohort: output/input_general_population.csv

generate_pneumonia_cohort:
run: cohortextractor:latest generate_cohort --study-definition study_definition_pneumonia
outputs:
highly_sensitive:
cohort: output/input_pneumonia.csv

matching:
run: python:latest python analysis/match_running.py
needs: [generate_covid_cohort, generate_covid_general_population_cohort]
outputs:
moderately_sensitive:
matching_report: output/matching_report_general_population.txt
highly_sensitive:
combined: output/matched_combined_general_population.csv

covid_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid"
needs: [generate_covid_cohort]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_covid.dta
moderately_sensitive:
out_dist: output/tabfig/outcomes_in_hosp_covid.csv
figs: output/tabfig/length_of_stay_covid.svg

covid_community_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "covid_community"
needs: [generate_covid_community_cohort]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_covid_community.dta

pneumonia_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "pneumonia"
needs: [generate_pneumonia_cohort]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_pneumonia.dta
moderately_sensitive:
out_dist: output/tabfig/outcomes_in_hosp_pneumonia.csv
figs: output/tabfig/length_of_stay_pneumonia.svg

gen_pop_rates_cohort:
run: stata-mp:latest analysis/000_cr_define_covariates_simple_rates.do "matched_combined_general_population"
needs: [matching]
outputs:
highly_sensitive:
analysis_dataset: output/cohort_rates_gen_population.dta

covid_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "covid"
needs: [covid_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid.csv

covid_comm_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "covid_community"
needs: [covid_community_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_covid_community.csv

pneumonia_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "pneumonia"
needs: [pneumonia_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_pneumonia.csv

gen_pop_rates:
run: stata-mp:latest analysis/201_cr_simple_rates.do "gen_population"
needs: [gen_pop_rates_cohort]
outputs:
moderately_sensitive:
rates: output/tabfig/rates_summary_gen_population.csv

baseline_characteristics:
run: stata-mp:latest analysis/400_baseline_characteristics.do
needs: [covid_rates_cohort, covid_community_rates_cohort, pneumonia_rates_cohort, gen_pop_rates_cohort]
outputs:
moderately_sensitive:
tables: output/tabfig/an_descriptiveTable_*.txt

append_cohorts:
run: stata-mp:latest analysis/300_cr_data_management_matching.do
needs: [covid_rates_cohort, pneumonia_rates_cohort, gen_pop_rates_cohort]
outputs:
moderately_sensitive:
log: output/append_cohorts.txt
highly_sensitive:
dataset: output/combined_covid_pneumonia.dta
dataset2: output/combined_covid_gen_population.dta

cox_models:
run: stata-mp:latest analysis/302_cox_models.do
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/cox_models.txt
dataset: output/tabfig/cox_model_summary.csv


fine_gray:
run: stata-mp:latest analysis/302_competing_events.do
needs: [append_cohorts]
outputs:
moderately_sensitive:
log: output/competing_events.txt
dataset: output/tabfig/fine_gray_summary.csv
figs: output/tabfig/cumInc_*.svg

Jobs

ID Status Action
7kdclqxjglfojoou succeeded generate_covid_cohort View
soa7r77w6rzfrwta succeeded generate_covid_community_cohort View
zmhni6izprsslftz succeeded generate_covid_general_population_cohort View
cfkaby27lv3ajnkv succeeded generate_pneumonia_cohort View
dbcnosz77m7dlt62 succeeded matching View
x3mkfcmqtcwtthbq succeeded covid_rates_cohort View
f2gf5hxu3srrshvm succeeded covid_community_rates_cohort View
chjqlr2lmw2nvyqc succeeded pneumonia_rates_cohort View
bio3b22s4p4qffsy succeeded gen_pop_rates_cohort View
jgnf6umh377vjumc succeeded covid_rates View
rsyr6rekugaoga6w succeeded covid_comm_rates View
u6z3l4xiacoawydg succeeded pneumonia_rates View
nm5sfvbkxpxwr3qv succeeded gen_pop_rates View
6wqzsxrezsqcljcv succeeded baseline_characteristics View
jktpbbu5aqeogl6p succeeded append_cohorts View
3ke7gyi25g7wasy6 succeeded cox_models View
qahi4k6md263okr3 succeeded fine_gray View