"{{ project_name }}.regions": "{{ regions }}", | "{{ project_name }}.regions": "{{ regions }}", | ||||
"{{ project_name }}.disk_size": "{{ disk_size }}", | "{{ project_name }}.disk_size": "{{ disk_size }}", | ||||
"{{ project_name }}.cluster_config": "{{ cluster_config }}" | "{{ project_name }}.cluster_config": "{{ cluster_config }}" | ||||
} | |||||
} | |||||
sample_id,recaled_bam,recaled_bam_index | |||||
CBCGA269277,oss://choppy-cromwell-result/test-choppy/PoN_test/0cb8780d-42f4-45d7-b36c-a8aaf6767eb2/call-BQSR/CBCGA269277_normal.sorted.deduped.realigned.recaled.bam,oss://choppy-cromwell-result/test-choppy/PoN_test/0cb8780d-42f4-45d7-b36c-a8aaf6767eb2/call-BQSR/CBCGA269277_normal.sorted.deduped.realigned.recaled.bam.bai |
fi | fi | ||||
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt $INTERVAL -r ${ref_dir}/${fasta} -i ${normal_bam} \ | ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt $INTERVAL -r ${ref_dir}/${fasta} -i ${normal_bam} \ | ||||
--algo TNhaplotyper2 --normal_sample ${sample} ${sample}.TNseq.PoN.vcf | |||||
--algo TNhaplotyper2 --tumor_sample ${sample} ${sample}.TNseq.PoN.vcf | |||||
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt $INTERVAL -r ${ref_dir}/${fasta} -i ${normal_bam} \ | ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt $INTERVAL -r ${ref_dir}/${fasta} -i ${normal_bam} \ | ||||
--algo TNscope --normal_sample ${sample} ${sample}.TNscope.PoN.vcf | |||||
--algo TNscope --tumor_sample ${sample} ${sample}.TNscope.PoN.vcf | |||||
>>> | >>> | ||||
runtime { | runtime { |