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joverlee521/vidrl-human-sera-ingest.smk

Last active August 29, 2024 18:04
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vidrl-human-sera-ingest
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vidrl-human-sera-ingest.smk
PREVIEW = config.get("preview", False)
YEAR = config.get("year", '2024')
VIDRL_PATH = "../fludata/VIDRL-Melbourne-WHO-CC/raw-data"
H1N1_PATH = f"{VIDRL_PATH}/A/H1N1pdm/HI"
H3N2_PATH = f"{VIDRL_PATH}/A/H3N2/HI"
H3N2_FRA = f"{VIDRL_PATH}/A/H3N2/FRA"
VIC_PATH = f"{VIDRL_PATH}/B/Victoria/HI"
H1N1_FSTEMS, = glob_wildcards(f"{H1N1_PATH}/{YEAR}/{{fstem}}.xlsx")
H3N2_FSTEMS, = glob_wildcards(f"{H3N2_PATH}/{YEAR}/{{fstem}}.xlsx")
H3N2_FRA_FSTEMS, = glob_wildcards(f"{H3N2_FRA}/{YEAR}/{{fstem}}.xlsx")
VIC_FSTEMs, = glob_wildcards(f"{VIC_PATH}/{YEAR}/{{fstem}}.xlsx")
rule ingest_all:
input:
h1n1pdm = expand("data/results/h1n1pdm/hi/{year}/{fstem}.done", year=[YEAR], fstem=H1N1_FSTEMS),
h3n2 = expand("data/results/h3n2/hi/{year}/{fstem}.done", year=[YEAR], fstem=H3N2_FSTEMS),
h3n2_fra = expand("data/results/h3n2/fra/{year}/{fstem}.done", year=[YEAR], fstem=H3N2_FRA_FSTEMS),
vix = expand("data/results/vic/hi/{year}/{fstem}.done", year=[YEAR], fstem=VIC_FSTEMs),
rule ingest_h1n1pdm:
input:
excel_worbook = f"{H1N1_PATH}/{{year}}/{{fstem}}.xlsx"
output:
touch("data/results/h1n1pdm/hi/{year}/{fstem}.done")
params:
h1n1_path = H1N1_PATH,
preview = "--preview" if PREVIEW else "",
log:
"data/logs/h1n1pdm/hi/{year}/{fstem}.log"
shell:
r"""
python3 tdb/vidrl_upload.py \
-db vidrl_tdb \
-v flu \
--subtype h1n1pdm \
--assay_type hi \
--path {params.h1n1_path}/{wildcards.year} \
--fstem {wildcards.fstem} \
--ftype vidrl \
--human-ref-only \
{params.preview} 2>&1 | tee {log}
"""
rule ingest_h3n2:
input:
excel_worbook = f"{H3N2_PATH}/{{year}}/{{fstem}}.xlsx"
output:
touch("data/results/h3n2/hi/{year}/{fstem}.done")
params:
h3n2_path = H3N2_PATH,
preview = "--preview" if PREVIEW else "",
log:
"data/logs/h3n2/hi/{year}/{fstem}.log"
shell:
r"""
python3 tdb/vidrl_upload.py \
-db vidrl_tdb \
-v flu \
--subtype h3n2 \
--assay_type hi \
--path {params.h3n2_path}/{wildcards.year} \
--fstem {wildcards.fstem} \
--ftype vidrl \
--human-ref-only \
{params.preview} 2>&1 | tee {log}
"""
rule ingest_h3n2_fra:
input:
excel_worbook = f"{H3N2_FRA}/{{year}}/{{fstem}}.xlsx"
output:
touch("data/results/h3n2/fra/{year}/{fstem}.done")
params:
h3n2_path = H3N2_FRA,
preview = "--preview" if PREVIEW else "",
log:
"data/logs/h3n2/fra/{year}/{fstem}.log"
shell:
r"""
python3 tdb/vidrl_upload.py \
-db vidrl_tdb \
-v flu \
--subtype h3n2 \
--assay_type fra \
--path {params.h3n2_path}/{wildcards.year} \
--fstem {wildcards.fstem} \
--ftype vidrl \
--human-ref-only \
{params.preview} 2>&1 | tee {log}
"""
rule ingest_vic:
input:
excel_worbook = f"{VIC_PATH}/{{year}}/{{fstem}}.xlsx"
output:
touch("data/results/vic/hi/{year}/{fstem}.done")
params:
vic_path = VIC_PATH,
preview = "--preview" if PREVIEW else "",
log:
"data/logs/vic/hi/{year}/{fstem}.log"
shell:
r"""
python3 tdb/vidrl_upload.py \
-db vidrl_tdb \
-v flu \
--subtype vic \
--assay_type hi \
--path {params.vic_path}/{wildcards.year} \
--fstem {wildcards.fstem} \
--ftype vidrl \
--human-ref-only \
{params.preview} 2>&1 | tee {log}
"""
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