LUYAO REN
4 years ago
2 changed files with 1 additions and 6 deletions
+ 1
- 1
tasks/merge_family.wdl
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| echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL5\tLCL6\tLCL7\tLCL8" > header_name | echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tLCL5\tLCL6\tLCL7\tLCL8" > header_name | ||||
| cat $a | grep '##' | cat - header_name > header | cat $a | grep '##' | cat - header_name > header | ||||
| paste LCL5.body LCL6.body LCL7.body LCL8.body > family.body | paste LCL5.body LCL6.body LCL7.body LCL8.body > family.body | ||||
| cat header family.body > ${project}.$rep_a.family.vcf | |||||
| cat header family.body > ${project}_$rep_a.family.vcf | |||||
| fi | fi | ||||
| done | done | ||||
| done | done |
+ 0
- 5
tasks/multiqc.wdl
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| set -e | set -e | ||||
| mkdir -p /cromwell_root/tmp/fastqc | mkdir -p /cromwell_root/tmp/fastqc | ||||
| mkdir -p /cromwell_root/tmp/fastqscreen | mkdir -p /cromwell_root/tmp/fastqscreen | ||||
| mkdir -p /cromwell_root/tmp/bamqc | |||||
| mkdir -p /cromwell_root/tmp/benchmark | mkdir -p /cromwell_root/tmp/benchmark | ||||
| cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc | cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc | ||||
| cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen | cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen | ||||
| cp ${sep=" " summary} /cromwell_root/tmp/benchmark | cp ${sep=" " summary} /cromwell_root/tmp/benchmark | ||||
| for i in ${sep=" " zip} | |||||
| do | |||||
| tar -zxvf $i -C /cromwell_root/tmp/bamqc | |||||
| done | |||||
| multiqc /cromwell_root/tmp/ | multiqc /cromwell_root/tmp/ | ||||
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