CNVkit/inputs

{
  "{{ project_name }}.sample_id": "{{ sample_id }}",
  "{{ project_name }}.normal_bam": {{ normal_bam | tojson }},
  "{{ project_name }}.normal_bai": {{ normal_bai | tojson }},
  "{{ project_name }}.tumor_bam": {{ tumor_bam | tojson }},
  "{{ project_name }}.tumor_bai": {{ tumor_bai | tojson }},
  "{{ project_name }}.fasta": "{{ fasta }}",
  "{{ project_name }}.faidx": "{{ faidx }}",
  "{{ project_name }}.ref_flat": "{{ ref_flat }}",
  "{{ project_name }}.method": "{{ method }}",
  "{{ project_name }}.reference": "{{ reference }}",
  "{{ project_name }}.docker": "{{ docker }}",
  "{{ project_name }}.bed": "{{ bed }}",
  "{{ project_name }}.disk_size": "{{ disk_size }}",
  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
  "{{ project_name }}.min_gap_size": "{{ min_gap_size }}"
}