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Fix bug: tumor_sample parameter

master
YaqingLiu před 4 roky
rodič
revize
ba5588de65
2 změnil soubory, kde provedl 7 přidání a 3 odebrání
  1. +5
    -1
      inputs
  2. +2
    -2
      tasks/PoN.wdl

+ 5
- 1
inputs Zobrazit soubor

"{{ 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

+ 2
- 2
tasks/PoN.wdl Zobrazit soubor

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 {

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