2 muutettua tiedostoa jossa 4 lisäystä ja 4 poistoa
+ 1
- 1
inputs
Näytä tiedosto
| "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}", | "{{ project_name }}.bcftools_docker": "{{ bcftools_docker }}", | ||||
| "{{ project_name }}.database": "{{ database }}", | "{{ project_name }}.database": "{{ database }}", | ||||
| "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}", | "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}", | ||||
| "{{ project_name }}.inputponfile": "oss://choppy-cromwell-result/test-choppy/FUSCC_TNBC_WES_liuyaqing_20200703/67f23290-260b-4f95-abce-7206f9e4e7fa/call-PON", | |||||
| "{{ project_name }}.inputponfile": "oss://choppy-cromwell-result/test-choppy/FUSCC_TNBC_WES_liuyaqing_20200703/vcf", | |||||
| "{{ project_name }}.regions": "{{ regions }}", | "{{ project_name }}.regions": "{{ regions }}", | ||||
| "{{ project_name }}.PONmode": "{{ PONmode }}", | "{{ project_name }}.PONmode": "{{ PONmode }}", | ||||
| "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}", | "{{ project_name }}.cosmic_vcf": "{{ cosmic_vcf }}", |
+ 3
- 3
tasks/bcftools.wdl
Näytä tiedosto
| if [ ${PONmode} ]; then | if [ ${PONmode} ]; then | ||||
| mkdir -p /cromwell_root/tmp/bcftools/ | mkdir -p /cromwell_root/tmp/bcftools/ | ||||
| cp ${pon_vcf}/*.vcf /cromwell_root/tmp/bcftools/ | |||||
| #for i in ${sep=" " pon_vcf} | #for i in ${sep=" " pon_vcf} | ||||
| #do | #do | ||||
| for i in /cromwell_root/tmp/bcftools/*.vcf | |||||
| for i in ${pon_vcf}/* | |||||
| do | do | ||||
| bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$i.gz | |||||
| cp $i /cromwell_root/tmp/bcftools/ | |||||
| bcftools view /cromwell_root/tmp/bcftools/$i -Oz -o /cromwell_root/tmp/bcftools/$i.gz | |||||
| done | done | ||||
| bcftools merge -m any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ | bcftools merge -m any -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ |
Loading…