test13

inputs

 {
   "{{ project_name }}.benchmarking_dir": "{{ benchmarking_dir }}",
   "{{ project_name }}.vcf_F7": "{{ vcf_F7 }}",
-  "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
   "{{ project_name }}.vcf_M8": "{{ vcf_M8 }}",
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.BENCHMARKdocker": "{{ BENCHMARKdocker }}",
   "{{ project_name }}.fastq_2_D5": "{{ fastq_2_D5 }}",
   "{{ project_name }}.FASTQSCREENdocker": "{{ FASTQSCREENdocker }}",
   "{{ project_name }}.fastq_2_F7": "{{ fastq_2_F7 }}",
-  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
   "{{ project_name }}.fastq_1_D6": "{{ fastq_1_D6 }}",
   "{{ project_name }}.fastq_1_F7": "{{ fastq_1_F7 }}",
-  "{{ project_name }}.SENTIEONdocker": "{{ SENTIEONdocker }}",
   "{{ project_name }}.REPLACE_SENTIEON_DOCKER": "{{ REPLACE_SENTIEON_DOCKER }}",
   "{{ project_name }}.DEEPVARIANT_DOCKER": "{{ DEEPVARIANT_DOCKER }}",
   "{{ project_name }}.QUALIMAPdocker": "{{ QUALIMAPdocker }}",

tasks/BQSR.wdl

 	
 	command <<<
 		set -o pipefail
-		set -e
-		/usr/local/gatk-4.4.0.0/gatk BaseRecalibrator \
-				-R ${ref_dir}/${fasta} \ 
-				-I ${realigned_bam} \
-				--known-sites ${dbsnp_dir}/${dbsnp}	\
-				--known-sites ${dbmills_dir}/${db_mills} \
-				-O ${sample}_recal_data.table
-		/usr/local/gatk-4.4.0.0/gatk ApplyBQSR \
-				-R ${ref_dir}/${fasta} \
-				-I ${realigned_bam} \
-				-bqsr ${sample}_recal_data.table \
-				-O ${sample}.sorted.deduped.realigned.recaled.bam
-		/usr/local/samtools-1.17/bin/samtools index -@ $(nproc) -o  ${sample}.sorted.deduped.realigned.recaled.bam.bai  ${sample}.sorted.deduped.realigned.recaled.bam
+        set -e
+        /usr/local/gatk-4.4.0.0/gatk BaseRecalibrator \
+            -R ${ref_dir}/${fasta} \
+            -I ${realigned_bam} \
+            --known-sites ${dbsnp_dir}/${dbsnp} \
+            --known-sites ${dbmills_dir}/${db_mills} \
+            -O ${sample}_recal_data.table
+
+        /usr/local/gatk-4.4.0.0/gatk ApplyBQSR \
+            -R ${ref_dir}/${fasta} \
+            -I ${realigned_bam} \
+            -bqsr ${sample}_recal_data.table \
+            -O ${sample}.sorted.deduped.realigned.recaled.bam
+
+        /usr/local/samtools-1.17/bin/samtools index -@ $(nproc) -o ${sample}.sorted.deduped.realigned.recaled.bam.bai ${sample}.sorted.deduped.realigned.recaled.bam
 	>>>
 	runtime {
 		docker:docker

tasks/Haplotyper.wdl

 			--reads=${recaled_bam} \
 			--output_vcf=${sample}_hc.vcf \
 			--num_shards=$(nproc) 
-		
+
 		/opt/gatk-4.4/gatk IndexFeatureFile -I ${sample}_hc.vcf -O ${sample}_hc.vcf.idx
 	>>>