LUYAO REN
преди 4 години
променени са 1 файла, в които са добавени 5 реда и са изтрити 5 реда
+ 5
- 5
tasks/delly.wdl
Целия файл
| nt=$(nproc) | nt=$(nproc) | ||||
| export OMP_NUM_THREADS=$nt | export OMP_NUM_THREADS=$nt | ||||
| /opt/delly/src/delly call -n -t DEL -g ${ref_dir}/${fasta} -o ${sample_name}.delly.del.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} | |||||
| /opt/delly/src/delly call -t DEL -g ${ref_dir}/${fasta} -o ${sample_name}.delly.del.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} | |||||
| /opt/delly/src/delly filter -t DEL -f somatic -o ${sample_name}.delly.del.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.del.somatic.bcf | /opt/delly/src/delly filter -t DEL -f somatic -o ${sample_name}.delly.del.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.del.somatic.bcf | ||||
| /opt/delly/src/delly call -n -t DUP -g ${ref_dir}/${fasta} -o ${sample_name}.delly.dup.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} | |||||
| /opt/delly/src/delly call -t DUP -g ${ref_dir}/${fasta} -o ${sample_name}.delly.dup.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} | |||||
| /opt/delly/src/delly filter -t DUP -f somatic -o ${sample_name}.delly.dup.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.dup.somatic.bcf | /opt/delly/src/delly filter -t DUP -f somatic -o ${sample_name}.delly.dup.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.dup.somatic.bcf | ||||
| /opt/delly/src/delly call -n -t INS -g ${ref_dir}/${fasta} -o ${sample_name}.delly.ins.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} | |||||
| /opt/delly/src/delly call -t INS -g ${ref_dir}/${fasta} -o ${sample_name}.delly.ins.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} | |||||
| /opt/delly/src/delly filter -t INS -f somatic -o ${sample_name}.delly.ins.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.ins.somatic.bcf | /opt/delly/src/delly filter -t INS -f somatic -o ${sample_name}.delly.ins.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.ins.somatic.bcf | ||||
| /opt/delly/src/delly call -n -t INV -g ${ref_dir}/${fasta} -o ${sample_name}.delly.inv.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} | |||||
| /opt/delly/src/delly call -t INV -g ${ref_dir}/${fasta} -o ${sample_name}.delly.inv.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} | |||||
| /opt/delly/src/delly filter -t INV -f somatic -o ${sample_name}.delly.inv.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.inv.somatic.bcf | /opt/delly/src/delly filter -t INV -f somatic -o ${sample_name}.delly.inv.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.inv.somatic.bcf | ||||
| /opt/delly/src/delly call -n -t BND -g ${ref_dir}/${fasta} -o ${sample_name}.delly.bnd.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} | |||||
| /opt/delly/src/delly call -t BND -g ${ref_dir}/${fasta} -o ${sample_name}.delly.bnd.somatic.bcf -x /opt/delly/excludeTemplates/human.hg38.excl.tsv ${tumor_bam} ${normal_bam} | |||||
| /opt/delly/src/delly filter -t BND -f somatic -o ${sample_name}.delly.bnd.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.bnd.somatic.bcf | /opt/delly/src/delly filter -t BND -f somatic -o ${sample_name}.delly.bnd.somatic.filtered.bcf -s samples.tsv ${sample_name}.delly.bnd.somatic.bcf | ||||
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