- name: multivcfanalyzer test_multivcfanalyzer
  command: nextflow run ./tests/modules/multivcfanalyzer -entry test_multivcfanalyzer -c ./tests/config/nextflow.config  -c ./tests/modules/multivcfanalyzer/nextflow.config
  tags:
    - multivcfanalyzer
  files:
    - path: output/multivcfanalyzer/MultiVCFAnalyzer.json
      md5sum: c841c9f04c6114911f308ea09a08980e
    - path: output/multivcfanalyzer/fullAlignment.fasta.gz
      contains:
        - ">Reference_MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome"
    - path: output/multivcfanalyzer/info.txt
      contains:
        - "Run finished"
    - path: output/multivcfanalyzer/snpAlignment.fasta.gz
      contains:
        - "test.vcf"
    - path: output/multivcfanalyzer/snpAlignmentIncludingRefGenome.fasta.gz
      contains:
        - ">Reference_MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome"
    - path: output/multivcfanalyzer/snpStatistics.tsv
      contains: ["statistics", "test.vcf", "test2.vcf"]
    - path: output/multivcfanalyzer/snpTable.tsv
      contains: ["Position", "test.vcf", "test2.vcf"]
    - path: output/multivcfanalyzer/snpTableForSnpEff.tsv
      md5sum: 8d7ab4ec98a89d290e301d6feae461aa
    - path: output/multivcfanalyzer/snpTableWithUncertaintyCalls.tsv
      contains: ["Position", "test.vcf", "test2.vcf"]
    - path: output/multivcfanalyzer/structureGenotypes.tsv
      contains: ["test.vcf", "test2.vcf"]
    - path: output/multivcfanalyzer/structureGenotypes_noMissingData-Columns.tsv
      contains: ["test.vcf", "test2.vcf"]