删除 'tasks/BQSR.wdl'

tasks/BQSR.wdl

@@ -1,66 +0,0 @@
-task BQSR {
-  
-  File ref_dir
-  File dbsnp_dir
-  File dbmills_dir
-  
-  String sample
-  String SENTIEON_LICENSE
-  String fasta
-  String dbsnp
-  String db_mills
-  File deduped_bam
-  File deduped_bam_index
-  String docker
-  String cluster_config
-  String disk_size
-
-  File? regions
-  Int? interval_padding
-  
-  command <<<
-    set -o pipefail
-    set -e
-    export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-    nt=$(nproc)
-
-    if [ ${regions} ]; then
-      INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
-    else
-      INTERVAL=""
-    fi
-
-    sentieon driver -t $nt \
-    -r ${ref_dir}/${fasta} -i ${deduped_bam} \
-    $INTERVAL \
-    --algo QualCal \
-    -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} \
-    ${sample}_recal_data.table
-
-    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 driver -t $nt --algo QualCal \
-    --plot --before ${sample}_recal_data.table --after ${sample}_recal_data.table.post ${sample}_recal_data.csv
-
-    sentieon plot bqsr -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
-  >>>
-
-  runtime {
-    docker: docker
-    cluster: cluster_config
-    systemDisk: "cloud_ssd 40"
-    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-  }
-
-  output {
-    File recal_table = "${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_data.csv"
-    File bqsrreport_pdf = "${sample}_bqsrreport.pdf"
-  }
-}