inputs

inputs

@@ -1,11 +1,11 @@
 {
   "{{ project_name }}.Dedup_bam": "{{ Dedup_bam }}",
-  "{{ project_name }}.fasta": "ucsc.hg19.chr20.unittest.fasta",
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
   "{{ project_name }}.disk_size": "500",
-  "{{ project_name }}.ref_fa_fai": "ucsc.hg19.chr20.unittest.fasta.fai",
+  "{{ project_name }}.ref_fa_fai": "GRCh38.d1.vd1.fa.fai",
   "{{ project_name }}.FBdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/freebayes:1.3.1",
   "{{ project_name }}.cluster_config": "OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc",
   "{{ project_name }}.Dedup_bam_index": "{{ Dedup_bam_index }}",
   "{{ project_name }}.sample": "{{ sample }}",
-  "{{ project_name }}.ref_dir": "oss://pgx-storage-backend/test_data/fsata/"
+  "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
 }

tasks/Freebayes.wdl

@@ -15,7 +15,7 @@ task Freebayes {
 		set -o pipefail
 		set -e	
 		nt=$(nproc)
-		/opt/freebayes/scripts/freebayes-parallel <(/opt/freebayes/scripts/fasta_generate_regions.py ${ref_dir}/${ref_fa_fai} 100) $nt -f ${ref_dir}/${fasta} --genotype-qualities ${Dedup_bam} > ${sample}_fb.vcf
+		/opt/freebayes/scripts/freebayes-parallel <(/opt/freebayes/scripts/fasta_generate_regions.py ${ref_dir}/${ref_fa_fai} 100000) $nt -f ${ref_dir}/${fasta} --genotype-qualities ${Dedup_bam} > ${sample}_fb.vcf
 	>>>
 
 	runtime {