LUYAO REN
5 年前
共有 2 个文件被更改，包括 2 次插入 和 2 次删除
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- 1
tasks/Freebayes.wdl
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| set -o pipefail | set -o pipefail | ||||
| set -e | set -e | ||||
| nt=$(nproc) | nt=$(nproc) | ||||
| freebayes -f ${ref_dir}/${fasta} --genotype-qualities --max-complex-gap ${half_read_length} ${chr_bam} > ${sample_name}_${chromosome}_fb.vcf | |||||
| /opt/freebayes/bin/freebayes -f ${ref_dir}/${fasta} --genotype-qualities --max-complex-gap ${half_read_length} ${chr_bam} > ${sample_name}_${chromosome}_fb.vcf | |||||
| >>> | >>> | ||||
| runtime { | runtime { |
+ 1
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tasks/breakChromo.wdl
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| } | } | ||||
| output { | output { | ||||
| File chr_bam = "${sample_name}_${chromosome}.bam" | File chr_bam = "${sample_name}_${chromosome}.bam" | ||||
| File chr_bam_bai = "samtools index ${sample_name}_${chromosome}.bam.bai" | |||||
| File chr_bam_bai = "${sample_name}_${chromosome}.bam.bai" | |||||
| } | } | ||||
| } | } |
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