Commit 05991fe8 authored by Chris Jewell's avatar Chris Jewell
Browse files

Created a data argument group in pipeline module

parent 9e3a9e78
......@@ -21,40 +21,44 @@ if __name__ == "__main__":
# Ruffus wrapper around argparse used to give us ruffus
# cmd line switches as well as our own config
argparser = rf.cmdline.get_argparse(description="COVID-19 pipeline")
argparser.add_argument(
data_args = argparser.add_argument_group(
"Data options", "Options controlling input data"
)
data_args.add_argument(
"-c",
"--config",
type=str,
help="global configuration file",
required=True,
)
argparser.add_argument(
data_args.add_argument(
"-r",
"--results-directory",
type=str,
help="pipeline results directory",
required=True,
)
argparser.add_argument(
data_args.add_argument(
"--date-range",
type=lambda s: datetime.datetime.strptime(s, '%Y-%m-%d'),
type=lambda s: datetime.datetime.strptime(s, "%Y-%m-%d"),
nargs=2,
help="Date range [low high)",
metavar="ISO6801",
)
argparser.add_argument(
data_args.add_argument(
"--reported-cases", type=str, help="Path to case file"
)
argparser.add_argument(
data_args.add_argument(
"--commute-volume", type=str, help="Path to commute volume file"
)
argparser.add_argument(
data_args.add_argument(
"--case-date-type",
type=str,
help="Case date type (specimen | report)",
choices=["specimen", "report"],
)
argparser.add_argument(
data_args.add_argument(
"--pillar", type=str, help="Pillar", choices=["both", "1", "2"]
)
......
......@@ -17,7 +17,7 @@ for PILLAR in both 1 2
do
for CASE_DATE_TYPE in specimen
do
RESULTS_DIR=$global_scratch/covid19/${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}
RESULTS_DIR=$global_scratch/covid19/${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}_nl
JOB_NAME="covid_${DATE_HIGH}_${PILLAR}_${CASE_DATE_TYPE}"
qsub -N $JOB_NAME covid_pipeline.sge \
--reported-cases "$CASES_FILE" \
......
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