test-integration.yml

- name: test-integration-GIAB-chrM
  tags:
    - integration
  command: >
    snakemake
    --configfile test/config/config-GIAB-chrM.json
    --use-singularity
    --singularity-args ' --containall --bind /tmp'
    --notemp
    --cores 1
    16699289_coverage.varda 16699289_variants.varda
  files:
    - path: 16699289_coverage.varda
    - path: 16699289_variants.varda

- name: test-trim-alt-exclude-uncalled
  tags:
    - integration
  command: >
    snakemake
    --configfile test/config/config-noalt-uncalled.json
    --use-singularity
    --singularity-args ' --containall --bind /tmp'
    --notemp
    --cores 1
    16699289_trimmed.vcf
  files:
    - path: 16699289_trimmed.vcf
      must_not_contain:
          - "chrM\t150\t.\tT\tC"
          - "chrM\t152\t.\tT\tC"
      contains:
          - "chrM\t73\t.\tG\tA"
          - "chrM\t150\t.\tT\t."
          - "chrM\t152\t.\tT\t."
          - "chrM\t195\t.\tC\tT"

- name: test-multiallelic
  tags:
    - integration
  command: >
    snakemake
    --configfile test/config/config-multiallelic.json
    --use-singularity
    --singularity-args ' --containall --bind /tmp'
    --notemp
    --cores 1
    16699289_variants_ucsc.varda
  files:
    - path: 16699289_trimmed.vcf
      must_not_contain:
          - "chrM\t195\t.\tC\tT,*"
          - "chrM\t410\t.\tA\tC,G"
          - "chrM\t2261\t.\tC\tT,CATTTT"
      contains:
          - "chrM\t195\t.\tC\t*"
          - "chrM\t410\t.\tA\tC"
          - "chrM\t2261\t.\tC\tT"
    - path: 16699289_single.vcf
    - path: 16699289_no_alt_star.vcf
      must_not_contain:
          - "chrM\t195\t.\tC\t*"
      contains:
          - "chrM\t152\t.\tT\tC"
          - "chrM\t410\t.\tA\tC"
    - path: 16699289_variants_ucsc.varda

- name: test-integration-GIAB-chrM-coverage
  tags:
    - integration
  command: >
    snakemake
    --configfile test/config/config-GIAB-chrM.json
    --use-singularity
    --singularity-args ' --containall --bind /tmp'
    --notemp
    --cores 1
    16699289_coverage.varda
  files:
    - path: 16699289_coverage.varda
      contains:
          - "NC_012920.1\t0\t16571\t2"