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new cromwell

master
huangyechao 1 year ago
parent
commit
ffe0529de3
12 changed files with 57 additions and 49 deletions
  1. +0
    -2
      README.md
  2. +1
    -1
      inputs
  3. +8
    -7
      tasks/BQSR.wdl
  4. +1
    -1
      tasks/Dedup.wdl
  5. +8
    -5
      tasks/Haplotyper.wdl
  6. +5
    -3
      tasks/Metrics.wdl
  7. +5
    -4
      tasks/Realigner.wdl
  8. +6
    -6
      tasks/TNscope.wdl
  9. +4
    -4
      tasks/TNseq.wdl
  10. +6
    -5
      tasks/corealigner.wdl
  11. +9
    -9
      tasks/deduped_Metrics.wdl
  12. +4
    -2
      tasks/mapping.wdl

+ 0
- 2
README.md View File

@@ -1,5 +1,3 @@
## README

**Author:** Huang Yechao

**E-mail:**17210700095@fudan.edu.cn

+ 1
- 1
inputs View File

@@ -7,7 +7,7 @@
"{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
"{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
"{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc' }}",
"{{ project_name }}.docker": "localhost:5000/sentieon-genomics:v2018.08.01 oss://pgx-docker-images/dockers",
"{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",
"{{ project_name }}.dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
"{{ project_name }}.sample": "{{ sample_name }}",
"{{ project_name }}.disk_size": "{{ disk_size }}",

+ 8
- 7
tasks/BQSR.wdl View File

@@ -1,11 +1,12 @@
task BQSR {
File ref_dir
File dbsnp_dir
File dbmills_dir
String sample
String SENTIEON_INSTALL_DIR
String fasta

File dbsnp_dir
String dbsnp
File dbmills_dir
String db_mills
File realigned_bam
File realigned_bam_index
@@ -31,10 +32,10 @@ task BQSR {

>>>
runtime {
dockerTag:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}

output {

+ 1
- 1
tasks/Dedup.wdl View File

@@ -19,7 +19,7 @@ task Dedup {
${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
>>>
runtime {
dockerTag:docker
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

+ 8
- 5
tasks/Haplotyper.wdl View File

@@ -1,11 +1,14 @@
task Haplotyper {
File ref_dir
File dbsnp_dir

String SENTIEON_INSTALL_DIR
String fasta
File recaled_bam
File recaled_bam_index
File dbsnp_dir
String dbsnp
File ref_dir
String sample
String docker
String cluster_config
@@ -20,15 +23,15 @@ command <<<
>>>
runtime {
dockerTag:docker
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}

output {
File vcf = "${sample}_hc.vcf"
File vcf_idx = "${sample}_hc.vcf.idx"
File vcf = "${sample}_hc.vcf"
File vcf_idx = "${sample}_hc.vcf.idx"
}
}


+ 5
- 3
tasks/Metrics.wdl View File

@@ -1,11 +1,13 @@
task Metrics{
task Metrics {


File ref_dir
String SENTIEON_INSTALL_DIR
String sample
String docker
String cluster_config

String fasta
File ref_dir
File sorted_bam
File sorted_bam_index
String disk_size
@@ -23,7 +25,7 @@ task Metrics{
>>>
runtime {
dockerTag:docker
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

+ 5
- 4
tasks/Realigner.wdl View File

@@ -1,13 +1,14 @@
task Realigner {

File ref_dir
File dbmills_dir

String SENTIEON_INSTALL_DIR
String sample
String fasta

File ref_dir
File Dedup_bam
File Dedup_bam_index
File dbmills_dir
String db_mills
String docker
String cluster_config
@@ -24,8 +25,8 @@ task Realigner {
>>>

runtime {
dockerTag:docker
cluster: cluster_config
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}

+ 6
- 6
tasks/TNscope.wdl View File

@@ -1,5 +1,9 @@
task {
task TNscope {

File ref_dir
File dbsnp_dir

String SENTIEON_INSTALL_DIR
String tumor_name
String normal_name
@@ -7,11 +11,8 @@ task {
String cluster_config

String fasta
File ref_dir

File corealigner_bam
File corealigner_bam_index
File dbsnp_dir
String dbsnp
String disk_size

@@ -34,7 +35,6 @@ task {
}

output {

File TNscope_vcf= "${sample}.TNscope.TN.vcf"
File TNscope_vcf_index = "${sample}.TNscope.TN.vcf.idx"
}

+ 4
- 4
tasks/TNseq.wdl View File

@@ -1,5 +1,8 @@
task {
task TNseq {
File ref_dir
File dbsnp_dir

String SENTIEON_INSTALL_DIR
String tumor_name
String normal_name
@@ -7,10 +10,8 @@ task {
String cluster_config

String fasta
File ref_dir
File corealigner_bam
File corealigner_bam_index
File dbsnp_dir
String dbsnp
String disk_size

@@ -33,7 +34,6 @@ task {
}

output {

File TNseq_vcf= "${sample}.TNseq.TN.vcf"
File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
}

+ 6
- 5
tasks/corealigner.wdl View File

@@ -1,15 +1,16 @@
task {
task corealigner {
File ref_dir
File dbsnp_dir
File dbmills_dir

String sample
String SENTIEON_INSTALL_DIR
String docker
String cluster_config
String fasta


File ref_dir
File dbsnp_dir
String dbsnp
File dbmills_dir
String db_mills
File tumor_recaled_bam
File tumor_recaled_bam_index

+ 9
- 9
tasks/deduped_Metrics.wdl View File

@@ -1,10 +1,10 @@
task deduped_Metrics {

File ref_dir
String SENTIEON_INSTALL_DIR
String sample

String fasta
File ref_dir
File Dedup_bam
File Dedup_bam_index
String docker
@@ -13,18 +13,18 @@ task deduped_Metrics {


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 ${Dedup_bam} --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt --algo QualDistribution ${sample}_deduped_qd_metrics.txt --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt --algo AlignmentStat ${sample}_deduped_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt
set -o pipefail
set -e
export SENTIEON_LICENSE=192.168.0.55:8990
nt=$(nproc)
${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo CoverageMetrics --omit_base_output ${sample}_deduped_coverage_metrics --algo MeanQualityByCycle ${sample}_deduped_mq_metrics.txt --algo QualDistribution ${sample}_deduped_qd_metrics.txt --algo GCBias --summary ${sample}_deduped_gc_summary.txt ${sample}_deduped_gc_metrics.txt --algo AlignmentStat ${sample}_deduped_aln_metrics.txt --algo InsertSizeMetricAlgo ${sample}_deduped_is_metrics.txt
>>>

runtime {
dockerTag:docker
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
}

output {

+ 4
- 2
tasks/mapping.wdl View File

@@ -1,6 +1,8 @@
task mapping {


File ref_dir
String fasta
File ref_dir
File fastq_1
File fastq_2

@@ -21,7 +23,7 @@ task mapping {
>>>

runtime {
dockerTag:docker
docker:docker
cluster: cluster_config
systemDisk: "cloud_ssd 40"
dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"

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