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Fix bug: BQSR.wdl

tags/v0.1.2
YaqingLiu hace 4 años
padre
commit
a6057601d2
Se han modificado 3 ficheros con 14 adiciones y 16 borrados
  1. +13
    -13
      tasks/BQSR.wdl
  2. +1
    -1
      tasks/Realigner.wdl
  3. +0
    -2
      workflow.wdl

+ 13
- 13
tasks/BQSR.wdl Ver fichero

String SENTIEON_INSTALL_DIR String SENTIEON_INSTALL_DIR
String SENTIEON_LICENSE String SENTIEON_LICENSE
String fasta String fasta
File? regions
String dbsnp String dbsnp
String db_mills String db_mills
File realigned_bam File realigned_bam
set -e set -e
export SENTIEON_LICENSE=${SENTIEON_LICENSE} export SENTIEON_LICENSE=${SENTIEON_LICENSE}
nt=$(nproc) nt=$(nproc)
if [ ${regions} != "" ]; then
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${realigned_bam} --interval ${regions} --algo QualCal -k ${dbsnp_dir}/${dbsnp} -k ${dbmills_dir}/${db_mills} ${sample}_recal_data.table
else
${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
fi
${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 bqsr -o ${sample}_bqsrreport.pdf ${sample}_recal_data.csv
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
-r ${ref_dir}/${fasta} -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_result.csv
${SENTIEON_INSTALL_DIR}/bin/sentieon plot QualCal -o ${sample}_bqsr.pdf ${sample}_recal_result.csv
>>> >>>
runtime { runtime {
File recal_post = "${sample}_recal_data.table.post" File recal_post = "${sample}_recal_data.table.post"
File recaled_bam = "${sample}.sorted.deduped.realigned.recaled.bam" File recaled_bam = "${sample}.sorted.deduped.realigned.recaled.bam"
File recaled_bam_index = "${sample}.sorted.deduped.realigned.recaled.bam.bai" File recaled_bam_index = "${sample}.sorted.deduped.realigned.recaled.bam.bai"
File recal_csv = "${sample}_recal_data.csv"
File bqsrreport_pdf = "${sample}_bqsrreport.pdf"
File recal_csv = "${sample}_recal_result.csv"
File bqsrreport_pdf = "${sample}_bqsr.pdf"
} }
} }

+ 1
- 1
tasks/Realigner.wdl Ver fichero

nt=$(nproc) nt=$(nproc)
if [ ${regions} ]; then if [ ${regions} ]; then
INTERVAL="--interval ${regions}"
INTERVAL="--interval_list ${regions}"
else else
INTERVAL="" INTERVAL=""
fi fi

+ 0
- 2
workflow.wdl Ver fichero

dbsnp=dbsnp, dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir, dbsnp_dir=dbsnp_dir,
sample=sample_id + '_tumor', sample=sample_id + '_tumor',
regions=regions,
docker=sentieon_docker, docker=sentieon_docker,
disk_size=disk_size, disk_size=disk_size,
cluster_config=cluster_config cluster_config=cluster_config
dbsnp=dbsnp, dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir, dbsnp_dir=dbsnp_dir,
sample=sample_id + '_normal', sample=sample_id + '_normal',
regions=regions,
docker=sentieon_docker, docker=sentieon_docker,
disk_size=disk_size, disk_size=disk_size,
cluster_config=cluster_config cluster_config=cluster_config

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