example-test-multi-sample.yaml

---
patient_id: 'TWGSAMIN000001'
# For multi samples, list the BAMs under the corresponding state (normal or tumor).
input:
  normal:
    - BAM: /hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam
  tumor:
    - BAM: /hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam
      contamination_table: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n2_getpileupsummaries_calculatecontamination.table
    - BAM: /hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam
      contamination_table: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n1_getpileupsummaries_calculatecontamination.table