test05

tasks/BQSR.wdl

@@ -17,14 +17,6 @@ task BQSR {
 	command <<<
 		set -o pipefail
 		set -e
-
-		# export SENTIEON_LICENSE=192.168.0.55:8990
-		# nt=$(nproc)
-		# ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table
-		# ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} -q ${sample}_recal_data.table --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table.post --algo ReadWriter ${sample}.sorted.deduped.realigned.recaled.bam
-		# ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --algo QualCal --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv
-		# ${SENTIEON_INSTALL_DIR}/bin/sentieon plot QualCal -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
-
 		gatk BaseRecalibrator \
 				-R ${ref_dir}/${fasta} \ 
 				-I ${realigned_bam} \
@@ -39,18 +31,6 @@ task BQSR {
 				-O ${sample}.sorted.deduped.realigned.recaled.bam
 		
 		samtools index -@ $(nproc) -o  ${sample}.sorted.deduped.realigned.recaled.bam.bai  ${sample}.sorted.deduped.realigned.recaled.bam
-		
-		# gatk BaseRecalibrator \
-		# 		-R ${ref_dir}/${fasta} \ 
-		# 		-I ${sample}.sorted.deduped.realigned.recaled.bam \
-		# 		--known-sites ${dbsnp_dir}/${dbsnp}	\
-		# 		--known-sites ${dbmills_dir}/${db_mills} \
-		# 		-O ${sample}_recal_data.table.post
-		
-		# gatk AnalyzeCovariates \
-		# 		-before ${sample}_recal_data.table \
-		# 		-after ${sample}_recal_data.table.post \
-		# 		-csv ${sample}_recal_data.csv
 	>>>
 	runtime {
 		docker:docker
@@ -60,11 +40,7 @@ task BQSR {
 	}
 
 	output {
-		# File recal_table = "${sample}_recal_data.table"
-		# File recal_post = "${sample}_recal_data.table.post"
 		File recaled_bam = "${sample}.sorted.deduped.realigned.recaled.bam"
 		File recaled_bam_index = "${sample}.sorted.deduped.realigned.recaled.bam.bai"
-		# File recal_csv = "${sample}_recal_data.csv"
-		# File bqsrreport_pdf = "${sample}_bqsrreport.pdf"
 	}
 }

tasks/Dedup.wdl

@@ -11,9 +11,6 @@ task Dedup {
 		set -o pipefail
 		set -e
 
-		nt=$(nproc)
-		# ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo LocusCollector --fun score_info ${sample}_score.txt
-		# ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -i ${sorted_bam} --algo Dedup --rmdup --score_info ${sample}_score.txt --metrics ${sample}_dedup_metrics.txt ${sample}.sorted.deduped.bam	
 		java -jar picard.jar  MarkDuplicates \
 					-I ${sorted_bam}  \
 					-O ${sample}.sorted.deduped.bam 
@@ -30,8 +27,6 @@ task Dedup {
 	}
 
 	output {
-		# File score = "${sample}_score.txt"
-		# File dedup_metrics = "${sample}_dedup_metrics.txt"
 		File Dedup_bam = "${sample}.sorted.deduped.bam"
 		File Dedup_bam_index = "${sample}.sorted.deduped.bam.bai"
 	}

tasks/Haplotyper.wdl

@@ -11,10 +11,6 @@ task Haplotyper {
 command <<<
 		set -o pipefail
 		set -e
-		# export SENTIEON_LICENSE=192.168.0.55:8990
-		# nt=$(nproc)	
-		# ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${recaled_bam} --algo Haplotyper ${sample}_hc.vcf
-
 		/opt/deepvariant/bin/run_deepvariant \
 			--model_type=WGS \
 			--ref=${ref_dir}/${fasta} \

tasks/deduped_Metrics.wdl

@@ -42,15 +42,6 @@ task deduped_Metrics {
 	}
 
 	output {
-		# File deduped_coverage_metrics_sample_summary = "${sample}_deduped_coverage_metrics.sample_summary"
-		# File deduped_coverage_metrics_sample_statistics = "${sample}_deduped_coverage_metrics.sample_statistics"
-		# File deduped_coverage_metrics_sample_interval_statistics = "${sample}_deduped_coverage_metrics.sample_interval_statistics"
-		# File deduped_coverage_metrics_sample_cumulative_coverage_proportions = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_proportions"
-		# File deduped_coverage_metrics_sample_cumulative_coverage_counts = "${sample}_deduped_coverage_metrics.sample_cumulative_coverage_counts"
-		# File deduped_mean_quality = "${sample}_deduped_mq_metrics.txt"
-		# File deduped_qd_metrics = "${sample}_deduped_qd_metrics.txt"
-		# File deduped_gc_summary = "${sample}_deduped_gc_summary.txt"
-		# File deduped_gc_metrics = "${sample}_deduped_gc_metrics.txt"
 		File dedeuped_aln_metrics = "${sample}_deduped_aln_metrics.txt"
 		File deduped_is_metrics = "${sample}_deduped_is_metrics.txt"
 		File deduped_QualityYield = "${sample}_deduped_QualityYield.txt"

tasks/get_variants_in_del.wdl

@@ -2,7 +2,7 @@ task adjust_mendelian_status_del {
 	File D5_trio_vcf
 	File D6_trio_vcf
 	File del_bed
-	String family_name = basename(D5_trio_vcf,".D5.vcf"
+	String family_name = basename(D5_trio_vcf,".D5.vcf")
 	String docker
 	String cluster_config
 	String disk_size

tasks/mapping.wdl

@@ -17,9 +17,6 @@ task mapping {
 	command <<<
 		set -o pipefail
 		set -e	
-		# export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		# nt=$(nproc)
-		# ${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${user_define_name}_${project}_${sample}.sorted.bam -t $nt --sam2bam -i -
 		bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $(nproc) -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} \
 			| samtools view -bS -@ $(nproc) - \
 			| samtools sort -@ $(nproc) -o ${user_define_name}_${project}_${sample}.sorted.bam -

tasks/sentieon.wdl

@@ -11,27 +11,14 @@ task sentieon {
 	command <<<
 		set -o pipefail	
 		set -e
-
-		# cat ${quality_yield} | sed -n '2,2p' > quality_yield.header
-		# cat ${quality_yield} | sed -n '3,3p' > ${sample}.quality_yield
 		cat ${quality_yield} | sed -n '7,7p' > quality_yield.header
 		cat ${quality_yield} | sed -n '8,8p' > ${sample}.quality_yield
-
-		# cat ${wgs_metrics_algo} | sed -n '2,2p' > wgs_metrics_algo.header
-		# cat ${wgs_metrics_algo} | sed -n '3,3p' > ${sample}.wgs_metrics_algo
 		cat ${wgs_metrics_algo} | sed -n '7,7p' > wgs_metrics_algo.header
 		cat ${wgs_metrics_algo} | sed -n '8,8p' > ${sample}.wgs_metrics_algo
-
-		# cat ${aln_metrics} | sed -n '2,2p'  > aln_metrics.header
-		# cat ${aln_metrics} | sed -n '5,5p'  > ${sample}.aln_metrics
 		cat ${aln_metrics} | sed -n '7,7p'  > aln_metrics.header
 		cat ${aln_metrics} | sed -n '10,10p'  > ${sample}.aln_metrics
-
-		# cat ${is_metrics} | sed -n '2,2p' > is_metrics.header
-		# cat ${is_metrics} | sed -n '3,3p' > ${sample}.is_metrics
 		cat ${is_metrics} | sed -n '7,7p' > is_metrics.header
 		cat ${is_metrics} | sed -n '8,8p' > ${sample}.is_metrics
-
 	>>>
 
 	runtime {