Update: simplify BQSR

tasks/BQSR.wdl

@@ -27,18 +27,6 @@ task BQSR {
     --algo QualCal \
     -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
     ${sample}_recal_data.table
-
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
-    -r ${ref_dir}/${fasta} -i ${deduped_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.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_result.csv
-    
-    ${SENTIEON_INSTALL_DIR}/bin/sentieon plot QualCal -o ${sample}_bqsr.pdf ${sample}_recal_result.csv
   >>>
 
   runtime {
@@ -50,10 +38,5 @@ task BQSR {
 
   output {
     File recal_table = "${sample}_recal_data.table"
-    File recal_post = "${sample}_recal_data.table.post"
-    File recaled_bam = "${sample}.sorted.deduped.recaled.bam"
-    File recaled_bam_index = "${sample}.sorted.deduped.recaled.bam.bai"
-    File recal_csv = "${sample}_recal_result.csv"
-    File bqsrreport_pdf = "${sample}_bqsr.pdf"
   }
 }