fasta location

inputs

@@ -2,10 +2,8 @@
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.docker": "{{ docker }}",
-  "{{ project_name }}.bam_index": "{{ bam_index }}",
   "{{ project_name }}.cluster_config": "{{ cluster_config }}",
-  "{{ project_name }}.bam": "{{ bam }}",
-  "{{ project_name }}.memory": "{{ memory }}",
+  "{{ project_name }}.vcf": "{{ vcf }}",
   "{{ project_name }}.sample": "{{ sample }}",
   "{{ project_name }}.ref_dir": "{{ ref_dir }}"
 }

tasks/pre.wdl

@@ -19,9 +19,9 @@ task pre {
 		export HGREF=/cromwell_root/tmp/reference_data/GRCh38.d1.vd1.fa
 
 		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
-			/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
 
 	>>>