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Adding example snakemake pipeline
Pushed from Domino: https://pharma.domino-eval.com/workspace/CDISC01_Team/CDISC01_RE_CSR?executionId=6511b9402c011115a15c032b
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‎Pipelines/Snakefile

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from domino import Domino
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from os import environ
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from os.path import splitext
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domino = Domino(
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f"{environ['DOMINO_PROJECT_OWNER']}/{environ['DOMINO_PROJECT_NAME']}"
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)
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def blocking_job(path):
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environments = {
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'.sas': "645163bc122db878f0012705"
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}
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file_name, file_ext = splitext(path)
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domino.job_start_blocking(
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command=path,
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environment_id=environments[file_ext]
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)
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report: "/mnt/data/CDISC01_RE_INTERIM/snakemake.rst"
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envvars:
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"DOMINO_USER_API_KEY",
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"DOMINO_API_HOST"
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rule all:
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input:
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"/mnt/data/ADAM/adae.sas7bdat",
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"/mnt/data/ADAM/adcm.sas7bdat",
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"/mnt/data/ADAM/adlb.sas7bdat",
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"/mnt/data/ADAM/admh.sas7bdat",
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"/mnt/data/ADAM/adsl.sas7bdat",
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"/mnt/data/ADAM/advs.sas7bdat",
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"/mnt/data/TFL/t_ae_rel.sas7bdat",
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"/mnt/data/TFL/t_pop.sas7bdat",
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"/mnt/data/TFL/t_vscat.sas7bdat",
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"/mnt/data/METADATA/t_ae_rel.sas7bdat",
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"/mnt/data/METADATA/t_pop.sas7bdat",
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"/mnt/data/METADATA/t_vscat.sas7bdat"
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rule metadata:
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input:
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"/mnt/code/import_metadata.sas",
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"/mnt/pvc-rev4-nfs/TFL_Metadata.xlsx"
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output:
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"/mnt/data/METADATA/t_ae_rel.sas7bdat",
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"/mnt/data/METADATA/t_pop.sas7bdat",
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"/mnt/data/METADATA/t_vscat.sas7bdat"
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log:
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"/mnt/artifacts/metadata.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule ADAE:
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input:
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"/mnt/code/prod/adam/ADAE.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/ae.sas7bdat",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/ex.sas7bdat",
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"/mnt/data/ADAM/adsl.sas7bdat"
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output:
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"/mnt/data/ADAM/adae.sas7bdat"
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log:
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"/mnt/artifacts/ADAE.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule ADCM:
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input:
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"/mnt/code/prod/adam/ADCM.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/cm.sas7bdat",
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"/mnt/data/ADAM/adsl.sas7bdat"
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output:
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"/mnt/data/ADAM/adcm.sas7bdat"
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log:
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"/mnt/artifacts/ADCM.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule ADLB:
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input:
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"/mnt/code/prod/adam/ADLB.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/lb.sas7bdat",
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"/mnt/data/ADAM/adsl.sas7bdat"
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output:
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"/mnt/data/ADAM/adlb.sas7bdat"
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log:
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"/mnt/artifacts/ADLB.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule ADMH:
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input:
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"/mnt/code/prod/adam/ADMH.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/mh.sas7bdat",
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"/mnt/data/ADAM/adsl.sas7bdat"
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output:
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"/mnt/data/ADAM/admh.sas7bdat"
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log:
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"/mnt/artifacts/ADMH.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule ADSL:
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input:
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"/mnt/code/prod/adam/ADSL.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/dm.sas7bdat"
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output:
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"/mnt/data/ADAM/adsl.sas7bdat"
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log:
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"/mnt/artifacts/ADSL.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule ADVS:
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input:
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"/mnt/code/prod/adam/ADVS.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/vs.sas7bdat",
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"/mnt/data/ADAM/adsl.sas7bdat"
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output:
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"/mnt/data/ADAM/advs.sas7bdat"
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log:
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"/mnt/artifacts/ADVS.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule t_ae_rel:
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input:
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"/mnt/code/prod/tfl/t_ae_rel.sas",
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"/mnt/data/METADATA/t_ae_rel.sas7bdat",
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"/mnt/data/ADAM/adsl.sas7bdat",
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"/mnt/data/ADAM/adae.sas7bdat"
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output:
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"/mnt/data/TFL/t_ae_rel.sas7bdat"
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log:
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"/mnt/artifacts/t_ae_rel.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule t_pop:
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input:
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"/mnt/code/prod/tfl/t_pop.sas",
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"/mnt/data/METADATA/t_pop.sas7bdat",
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"/mnt/data/ADAM/adsl.sas7bdat"
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output:
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"/mnt/data/TFL/t_pop.sas7bdat"
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log:
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"/mnt/artifacts/t_pop.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule t_vscat:
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input:
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"/mnt/code/prod/tfl/t_vscat.sas",
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"/mnt/data/METADATA/t_vscat.sas7bdat",
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"/mnt/data/ADAM/advs.sas7bdat"
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output:
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"/mnt/data/TFL/t_vscat.sas7bdat"
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log:
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"/mnt/artifacts/t_vscat.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule qc_ADAE:
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input:
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"/mnt/code/qc/adam/qc_ADAE.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/ae.sas7bdat",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/ex.sas7bdat",
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"/mnt/data/ADAM/adae.sas7bdat",
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"/mnt/data/ADAMQC/adsl.sas7bdat"
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log:
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"/mnt/artifacts/qc_ADAE.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule qc_ADCM:
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input:
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"/mnt/code/qc/adam/qc_ADCM.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/cm.sas7bdat",
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"/mnt/data/ADAM/adcm.sas7bdat",
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"/mnt/data/ADAMQC/adsl.sas7bdat"
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log:
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"/mnt/artifacts/qc_ADCM.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule qc_ADLB:
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input:
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"/mnt/code/qc/adam/qc_ADLB.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/lb.sas7bdat",
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"/mnt/data/ADAM/adlb.sas7bdat",
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"/mnt/data/ADAMQC/adsl.sas7bdat"
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log:
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"/mnt/artifacts/qc_ADLB.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule qc_ADMH:
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input:
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"/mnt/code/qc/adam/qc_ADMH.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/mh.sas7bdat",
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"/mnt/data/ADAM/admh.sas7bdat",
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"/mnt/data/ADAMQC/adsl.sas7bdat"
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log:
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"/mnt/artifacts/qc_ADMH.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule qc_ADSL:
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input:
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"/mnt/code/qc/adam/qc_ADSL.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/dm.sas7bdat",
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"/mnt/data/ADAM/adsl.sas7bdat"
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log:
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"/mnt/artifacts/qc_ADSL.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule qc_ADVS:
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input:
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"/mnt/code/qc/adam/qc_ADVS.sas",
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"/mnt/imported/data/snapshots/SDTMBLIND/MAY162023/vs.sas7bdat",
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"/mnt/data/ADAM/advs.sas7bdat",
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"/mnt/data/ADAMQC/adsl.sas7bdat"
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log:
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"/mnt/artifacts/qc_ADVS.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule qc_t_ae_rel:
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input:
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"/mnt/code/qc/tfl/qc_t_ae_rel.sas",
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"/mnt/data/ADAM/adsl.sas7bdat",
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"/mnt/data/ADAM/adae.sas7bdat"
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log:
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"/mnt/artifacts/qc_t_ae_rel.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule qc_t_pop:
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input:
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"/mnt/code/qc/tfl/qc_t_pop.sas",
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"/mnt/data/ADAM/adsl.sas7bdat"
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log:
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"/mnt/artifacts/qc_t_pop.log"
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run:
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run = blocking_job(input[0])
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print(run)
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rule qc_t_vscat:
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input:
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"/mnt/code/qc/tfl/qc_t_vscat.sas",
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"/mnt/data/ADAM/advs.sas7bdat"
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log:
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"/mnt/artifacts/qc_t_vscat.log"
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run:
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run = blocking_job(input[0])
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print(run)

‎Pipelines/snakemake.sh

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touch /mnt/data/$DOMINO_PROJECT_NAME/snakemake.rst
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snakemake --cores 1 --directory "/mnt/data/$DOMINO_PROJECT_NAME/" && snakemake --report "/mnt/data/$DOMINO_PROJECT_NAME/report.html" --directory "/mnt/data/$DOMINO_PROJECT_NAME/"

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