TNScope_and_Stralka/inputs

{
"{{ project_name }}.sample_id": "{{ sample_id }}",
"{{ project_name }}.normal_deduped_bam": "{{ normal_deduped_bam }}",
"{{ project_name }}.normal_deduped_bam_bai": "{{ normal_deduped_bam_bai }}",
"{{ project_name }}.tumor_deduped_bam": "{{ tumor_deduped_bam }}",
"{{ project_name }}.tumor_deduped_bam_bai": "{{ tumor_deduped_bam_bai }}",
"{{ project_name }}.Seq_platform": "{{ Seq_platform }}",
"{{ project_name }}.ref_fasta": "{{ ref_fasta }}",
"{{ project_name }}.ref_fasta_dir": "{{ ref_fasta_dir }}",
"{{ project_name }}.fastqc": {{ fastqc | tojson }},
"{{ project_name }}.cluster_config": "{{cluster_config }}",
"{{ project_name }}.disk_size": "{{ disk_size }}",
"{{ project_name }}.docker_fastp": "{{ docker_fastp }}",
"{{ project_name }}.docker_sentieon": "{{ docker_sentieon }}",
"{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
"{{ project_name }}.docker_qualimap": "{{ docker_qualimap }}",
"{{ project_name }}.annot_gff": "{{ annot_gff }}",
"{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",
"{{ project_name }}.dbmills_dir": "{{ dbmills_dir }}",
"{{ project_name }}.dbsnp": "{{ dbsnp }}",
"{{ project_name }}.db_mills": "{{ db_mills }}",
"{{ project_name }}.bamqc": {{ bamqc | tojson }},
"{{ project_name }}.germline_resource": "{{ germline_resource }}",
"{{ project_name }}.germline_resource_tbi": "{{ germline_resource_tbi }}",
"{{ project_name }}.docker_manta": "{{ docker_manta }}",
"{{ project_name }}.docker_strelka": "{{ docker_strelka }}",
"{{ project_name }}.annovar_database": "{{ annovar_database}}",
"{{ project_name }}.docker_bcftools":"{{docker_bcftools}}",
"{{ project_name }}.docker_annovar":"{{docker_annovar}}",
"{{ project_name }}.Annovar":{{ Annovar | tojson }},
"{{ project_name }}.AF_filter":{{ AF_filter | tojson }},
"{{ project_name }}.regions":"{{regions}}",
"{{ project_name }}.baseline":"{{baseline}}",
"{{ project_name }}.hg38_CDS":"{{hg38_CDS}}",
"{{ project_name }}.docker_tmb": "{{ docker_tmb }}",
"{{ project_name }}.docker_MSIsensor": "{{ docker_MSIsensor }}",
"{{ project_name }}.tumor_recal_table": "{{ tumor_recal_table }}",
"{{ project_name }}.normal_recal_table": "{{ normal_recal_table }}"

}