variant-calling/inputs

{
  "{{ project_name }}.sample_id": "{{ sample_id }}",
  "{{ project_name }}.tumor_fastq_1": "{{ tumor_fastq_1 }}",
  "{{ project_name }}.tumor_fastq_2": "{{ tumor_fastq_2 }}",
  "{{ project_name }}.normal_fastq_1": "{{ normal_fastq_1 }}",
  "{{ project_name }}.normal_fastq_2": "{{ normal_fastq_2 }}",
  "{{ project_name }}.fasta": "{{ fasta }}",
  "{{ project_name }}.ref_dir": "{{ ref_dir }}",
  "{{ project_name }}.dbsnp": "{{ dbsnp }}",
  "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
  "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
  "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
  "{{ project_name }}.db_mills": "{{ db_mills }}",
  "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
  "{{ project_name }}.varscan_docker": "{{ varscan_docker }}",
  "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
  "{{ project_name }}.maftools_docker": "{{ maftools_docker }}",
  "{{ project_name }}.database": "{{ database }}",
  "{{ project_name }}.regions": "{{ regions }}",
  "{{ project_name }}.set_pon": {{ set_pon }},
  "{{ project_name }}.pon_vcf": "{{ pon_vcf }}",
  "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}",
  "{{ project_name }}.cosmic_dir": "{{ cosmic_dir }}",
  "{{ project_name }}.disk_size": "{{ disk_size }}",
  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
  "{{ project_name }}.germline": {{ germline }},
  "{{ project_name }}.TNseq": {{ TNseq }},
  "{{ project_name }}.TNscope": {{ TNscope }},
  "{{ project_name }}.Varscan": {{ Varscan }}
}