LUYAO REN
3 years ago
2 changed files with 3 additions and 5 deletions
+ 1
- 3
inputs
View File
| "{{ project_name }}.fasta": "{{ fasta }}", | "{{ project_name }}.fasta": "{{ fasta }}", | ||||
| "{{ project_name }}.disk_size": "{{ disk_size }}", | "{{ project_name }}.disk_size": "{{ disk_size }}", | ||||
| "{{ project_name }}.docker": "{{ docker }}", | "{{ project_name }}.docker": "{{ docker }}", | ||||
| "{{ project_name }}.bam_index": "{{ bam_index }}", | |||||
| "{{ project_name }}.cluster_config": "{{ cluster_config }}", | "{{ project_name }}.cluster_config": "{{ cluster_config }}", | ||||
| "{{ project_name }}.bam": "{{ bam }}", | |||||
| "{{ project_name }}.memory": "{{ memory }}", | |||||
| "{{ project_name }}.vcf": "{{ vcf }}", | |||||
| "{{ project_name }}.sample": "{{ sample }}", | "{{ project_name }}.sample": "{{ sample }}", | ||||
| "{{ project_name }}.ref_dir": "{{ ref_dir }}" | "{{ project_name }}.ref_dir": "{{ ref_dir }}" | ||||
| } | } |
+ 2
- 2
tasks/pre.wdl
View File
| export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa | export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa | ||||
| if [[ ${sample} =~ "LCL7" ]]; then | if [[ ${sample} =~ "LCL7" ]]; then | ||||
| /opt/hap.py/bin/pre.py ${vcf} ${sample}.vcf.gz -r ${ref_dir}/${fasta} -D -L --fixchr --gender male --threads $nt --logfile ${sample}.vairants.normalization.pre.log | |||||
| /opt/hap.py/bin/pre.py ${vcf} ${sample}.vcf.gz -r /cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa -D -L --fixchr --gender male --threads $nt --logfile ${sample}.vairants.normalization.pre.log | |||||
| else | else | ||||
| /opt/hap.py/bin/pre.py ${vcf} ${sample}.vcf.gz -r ${ref_dir}/${fasta} -D -L --fixchr --gender female --threads $nt --logfile ${sample}.vairants.normalization.pre.log | |||||
| /opt/hap.py/bin/pre.py ${vcf} ${sample}.vcf.gz -r /cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa -D -L --fixchr --gender female --threads $nt --logfile ${sample}.vairants.normalization.pre.log | |||||
| fi | fi | ||||
| >>> | >>> |
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