WesPipe-hg19-bam/inputs

{
  "{{ project_name }}.sample_id": "{{ sample_id }}",
  "{{ project_name }}.tumor_bam": "{{ tumor_bam }}",
  "{{ project_name }}.tumor_bam_index": "{{ tumor_bam_index }}",
  "{{ project_name }}.normal_bam": "{{ normal_bam }}",
  "{{ project_name }}.normal_bam_index": "{{ normal_bam_index }}",
  "{{ project_name }}.read_structure": "{{ read_structure }}",
  "{{ project_name }}.duplex_umi": "{{ duplex_umi }}",
  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
  "{{ project_name }}.sentieon_docker": "{{ sentieon_docker }}",
  "{{ project_name }}.varscan_docker": "{{ varscan_docker }}",
  "{{ project_name }}.manta_docker": "{{ manta_docker }}",
  "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}",
  "{{ project_name }}.annovar_docker": "{{ annovar_docker }}",
  "{{ project_name }}.annotsv_docker": "{{ annotsv_docker }}",
  "{{ project_name }}.cnvkit_docker": "{{ cnvkit_docker }}",
  "{{ project_name }}.sequenza_docker": "{{ sequenza_docker }}",
  "{{ project_name }}.msisensor_docker": "{{ msisensor_docker }}",
  "{{ project_name }}.tmb_docker": "{{ tmb_docker }}",
  "{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
  "{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
  "{{ project_name }}.qualimap_docker": "{{ qualimap_docker }}",
  "{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
  "{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
  "{{ project_name }}.platform": "{{ platform }}",
  "{{ 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 }}.annovar_database": "{{ annovar_database }}",
  "{{ project_name }}.annotsv_database": "{{ annotsv_database }}",
  "{{ project_name }}.gc": "{{ gc }}",
  "{{ project_name }}.baseline": "{{ baseline }}",
  "{{ project_name }}.ref_flat": "{{ ref_flat }}",
  "{{ project_name }}.disk_size": "{{ disk_size }}",
  "{{ project_name }}.cluster_2cpu_4gb": "{{ cluster_2cpu_4gb }}",
  "{{ project_name }}.cluster_16cpu_32gb": "{{ cluster_16cpu_32gb }}",
  "{{ project_name }}.qc": {{ qc | tojson }},
  "{{ project_name }}.multi_caller": {{ multi_caller | tojson }}
}