indent using 2 spaces

defaults

@@ -1,25 +1,25 @@
 {
-    "fasta": "GRCh38.d1.vd1.fa",
-    "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-    "dbsnp": "dbsnp_146.hg38.vcf",
-    "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-    "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
-    "SENTIEON_LICENSE": "192.168.0.55:8990",
-    "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-    "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
-    "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2020.10.07",
-    "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
-    "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
-    "maftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/r-base:4.0.2",
-    "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
-    "database": "oss://pgx-reference-data/annovar_hg38/",
-    "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed",
-    "set_pon": "true",
-    "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",
-    "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
-    "disk_size": "200",
-    "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-    "set_annovar": "true",
-    "set_vcf2maf": "true",
-    "germline": "false"
+  "fasta": "GRCh38.d1.vd1.fa",
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "dbsnp": "dbsnp_146.hg38.vcf",
+  "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "SENTIEON_LICENSE": "192.168.0.55:8990",
+  "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
+  "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2020.10.07",
+  "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
+  "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
+  "maftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/r-base:4.0.2",
+  "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
+  "database": "oss://pgx-reference-data/annovar_hg38/",
+  "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed",
+  "set_pon": "true",
+  "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",
+  "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
+  "disk_size": "200",
+  "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
+  "set_annovar": "true",
+  "set_vcf2maf": "true",
+  "germline": "false"
 }

tasks/PoN.wdl

@@ -1,51 +1,51 @@
 task PoN {
 
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	File ref_dir
-	String fasta
-	File cosmic_dir
-	String cosmic_vcf
-	File dbsnp_dir
-	String dbsnp
-	File regions
+  String SENTIEON_INSTALL_DIR
+  String SENTIEON_LICENSE
+  File ref_dir
+  String fasta
+  File cosmic_dir
+  String cosmic_vcf
+  File dbsnp_dir
+  String dbsnp
+  File regions
 
-	File normal_bam
-	File normal_bam_index
-	String sample=basename(normal_bam, ".*")
-	String docker
-	String cluster_config
-	String disk_size
-	
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp/cosmic/
-		cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/cosmic/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/cosmic/${cosmic_vcf}
+  File normal_bam
+  File normal_bam_index
+  String sample=basename(normal_bam, ".*")
+  String docker
+  String cluster_config
+  String disk_size
+  
+  command <<<
+    set -o pipefail
+    set -e
+    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+    nt=$(nproc)
+    mkdir -p /cromwell_root/tmp/cosmic/
+    cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/cosmic/
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/cosmic/${cosmic_vcf}
 
-		# Generating TNhaplotyper PoN
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNhaplotyper --detect_pon --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}_TNhaplotyper_pon.vcf
+    # Generating TNhaplotyper PoN
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNhaplotyper --detect_pon --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}_TNhaplotyper_pon.vcf
 
-		# Generating TNhaplotyper2 PoN
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNhaplotyper2 --normal_sample ${sample} ${sample}_TNhaplotyper2_pon.vcf
+    # Generating TNhaplotyper2 PoN
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNhaplotyper2 --normal_sample ${sample} ${sample}_TNhaplotyper2_pon.vcf
 
-		# Generating TNscope PoN
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNscope --normal_sample ${sample} ${sample}_TNscope_pon.vcf
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	
-	}
+    # Generating TNscope PoN
+    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${normal_bam} --algo TNscope --normal_sample ${sample} ${sample}_TNscope_pon.vcf
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"  
+  }
 
-	output {
-		File TNhaplotyper_pon_vcf = "${sample}_TNhaplotyper_pon.vcf"
-		File TNhaplotyper2_pon_vcf = "${sample}_TNhaplotyper2_pon.vcf"
-		File TNscope_pon_vcf = "${sample}_TNscope_pon.vcf"
-	}
+  output {
+    File TNhaplotyper_pon_vcf = "${sample}_TNhaplotyper_pon.vcf"
+    File TNhaplotyper2_pon_vcf = "${sample}_TNhaplotyper2_pon.vcf"
+    File TNscope_pon_vcf = "${sample}_TNscope_pon.vcf"
+  }
 }

tasks/mergePoN.wdl

@@ -1,33 +1,33 @@
 task mergePoN {
 
-	Array[File] pon_vcfs
-	String panel_id
-	String docker
-	String cluster_config
-	String disk_size
+  Array[File] pon_vcfs
+  String panel_id
+  String docker
+  String cluster_config
+  String disk_size
 
-	command <<<
-		set -o pipefail
-		set -e
-		mkdir -p /cromwell_root/tmp/bcftools
+  command <<<
+    set -o pipefail
+    set -e
+    mkdir -p /cromwell_root/tmp/bcftools
 
-		for i in ${sep=" " pon_vcfs}
-		do
-			bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz)
-			bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f
-		done
+    for i in ${sep=" " pon_vcfs}
+    do
+      bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz)
+      bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f
+    done
 
-		bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > ${panel_id}_pon.vcf
-	>>>
+    bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > ${panel_id}_pon.vcf
+  >>>
 
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	
-	output {
-		File panel_of_normal_vcf = "${panel_id}_pon.vcf"
-	}
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File panel_of_normal_vcf = "${panel_id}_pon.vcf"
+  }
 }