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 }}.tumor_deduped_bam": "{{ tumor_deduped_bam }}",
  "{{ project_name }}.normal_deduped_bam": "{{ normal_deduped_bam }}",
  "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
  "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
  "{{ project_name }}.varscan_docker": "{{ varscan_docker }}",
  "{{ project_name }}.pindel_docker": "{{ pindel_docker }}",
  "{{ project_name }}.samtools_docker": "{{ samtools_docker }}",
  "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
  "{{ project_name }}.pl": "{{ pl }}",
  "{{ project_name }}.fasta": "{{ fasta }}",
  "{{ project_name }}.ref_dir": "{{ ref_dir }}",
  "{{ project_name }}.dbsnp": "{{ dbsnp }}",
  "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
  "{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
  "{{ project_name }}.db_mills": "{{ db_mills }}",
  "{{ project_name }}.germline_resource": "{{ germline_resource }}",
  "{{ project_name }}.germline_resource_tbi": "{{ germline_resource_tbi }}",
  "{{ project_name }}.regions": "{{ regions }}",
  "{{ project_name }}.interval_padding": "{{ interval_padding }}",
  "{{ project_name }}.hg": "{{ hg }}",
  "{{ project_name }}.annovar_database": "{{ annovar_database }}",
  "{{ project_name }}.tnseq_pon": "{{ tnseq_pon }}",
  "{{ project_name }}.tnscope_pon": "{{ tnscope_pon }}",
  "{{ project_name }}.vep_path": "{{ vep_path }}",
  "{{ project_name }}.cache": "{{ cache }}",
  "{{ project_name }}.species": "{{ species }}",
  "{{ project_name }}.vcf2maf_path": "{{ vcf2maf_path }}",
  "{{ project_name }}.vep_docker": "{{ vep_docker }}",
  "{{ project_name }}.disk_size": "{{ disk_size }}",
  "{{ project_name }}.cluster_config": "{{ cluster_config }}",
  "{{ project_name }}.haplotyper": {{ haplotyper | tojson }},
  "{{ project_name }}.pindel": {{ pindel | tojson }},
  "{{ project_name }}.tnseq": {{ tnseq | tojson }},
  "{{ project_name }}.tnscope": {{ tnscope | tojson }},
  "{{ project_name }}.varscan": {{ varscan | tojson }},
  "{{ project_name }}.annovar": {{ annovar | tojson }},
  "{{ project_name }}.only_pass": {{ only_pass | tojson }},
  "{{ project_name }}.vep": {{ vep | tojson }},
  "{{ project_name }}.input_fastq": {{ input_fastq | tojson }},
  "{{ project_name }}.input_bam": {{ input_bam | tojson }}
}