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Fix bug: TNseq.wdl

master
YaqingLiu 4 vuotta sitten
vanhempi
commit
d0ab58508f
1 muutettua tiedostoa jossa 3 lisäystä ja 3 poistoa
  1. +3
    -3
      tasks/TNseq.wdl

+ 3
- 3
tasks/TNseq.wdl Näytä tiedosto

--tumor_segments ${sample}.contamination.segments \ --tumor_segments ${sample}.contamination.segments \
${sample}.contamination ${sample}.contamination
sentieon driver -r REFERENCE \
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r REFERENCE \
--algo TNfilter \ --algo TNfilter \
--tumor_sample ${tumor_name} --normal_sample ${normal_name} \ --tumor_sample ${tumor_name} --normal_sample ${normal_name} \
-v ${sample}.TNseq.TN.tmp.vcf \ -v ${sample}.TNseq.TN.tmp.vcf \
} }


output { output {
File TNseq_vcf = "${sample}.TNseq.TN.vcf"
File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
File contamination = "${sample}.contamination" File contamination = "${sample}.contamination"
File contamination_segments = "${sample}.contamination.segments" File contamination_segments = "${sample}.contamination.segments"
File orientation = "${sample}.orientation" File orientation = "${sample}.orientation"
File TNseq_vcf = "${sample}.TNseq.TN.vcf"
File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
} }
} }

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