test_concat_germline_vcfs.yml

- name: Run all germline variant callers and check for existence of concatenated vcf-files
  command: nextflow run main.nf -profile test --input ./tests/csv/3.0/mapped_joint_bam.csv --concatenate_vcfs --tools deepvariant,freebayes,haplotypecaller,manta,mpileup,strelka,tiddit --step variant_calling --outdir results
  tags:
    - concatenate_vcfs
  files:
    - path: results/variant_calling/concat/testN/testN.germline.vcf.gz
      # binary changes md5sums on reruns
      contains:
        [
          "SOURCE=testN.deepvariant.vcf.gz",
          "AB=0.167832;ABP=277.102;AC=1;AF=0.5;AN=2;AO=48;CIGAR=1X;DP=286;DPB=286;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=105.855;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=2017;QR=9863;RO=238;RPL=0;RPP=107.241;RPPR=519.821;RPR=48;RUN=1;SAF=24;SAP=3.0103;SAR=24;SRF=119;SRP=3.0103;SRR=119;TYPE=snp;technology.illumina=1;",
          "SOURCE=testN.freebayes.vcf.gz",
          "SNVHPOL=7;MQ=60;",
          "SOURCE=testN.strelka.variants.vcf.gz",
          "SOURCE=testN.bcftools.vcf.gz",
        ]
    - path: results/variant_calling/concat/testT/testT.germline.vcf.gz
    # binary changes md5sums on reruns
    - path: results/variant_calling/concat/testN/testN.germline.vcf.gz.tbi
    # binary changes md5sums on reruns
    - path: results/variant_calling/concat/testT/testT.germline.vcf.gz.tbi
    # binary changes md5sums on reruns