test_integration_run.yml 1.11 KB
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- name: test-integration-run
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  command: >-
    bash -c '
    snakemake --use-conda --conda-prefix ${CONDA_PREFIX} --jobs 100 -w 120
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    --cluster "sbatch --parsable" -r -p -s Snakefile
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    --config REFERENCE=tests/data/ref.fa GATK=${GATK_JAR}
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    DBSNP=tests/data/database.vcf.gz
    ONETHOUSAND=tests/data/database.vcf.gz
    HAPMAP=tests/data/database.vcf.gz
    SAMPLE_CONFIG=tests/data/sample_config.json'
  exit_code: 0
  stderr:
    contains:
      - "Job counts"
      - "localrule all:"
      - "(100%) done"
    must_not_contain:
      - "rror"
  tags:
    - integration
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- name: test-singularity-integration-no-cluster
  command: >-
    bash -c '
    snakemake --singularity --jobs 100 -w 120
    -r -p -s Snakefile
    --config REFERENCE=tests/data/ref.fa GATK=tests/data/ref.fa
    DBSNP=tests/data/database.vcf.gz
    ONETHOUSAND=tests/data/database.vcf.gz
    HAPMAP=tests/data/database.vcf.gz
    SAMPLE_CONFIG=tests/data/sample_config.json'
  exit_code: 0
  stderr:
    contains:
      - "Job counts"
      - "localrule all:"
      - "(100%) done"
    must_not_contain:
      - "rror"
  tags:
    - singularity-integration