Browse Source

Fix bug: sample_id

master
YaqingLiu 4 years ago
parent
commit
d04660eabe
3 changed files with 6 additions and 5 deletions
  1. +1
    -1
      inputs
  2. +1
    -1
      tasks/PoN.wdl
  3. +4
    -3
      workflow.wdl

+ 1
- 1
inputs View File

{ {
"{{ project_name }}.panel_id": "{{ panel_id }}",
"{{ project_name }}.sample_id": "{{ sample_id }}",
"{{ project_name }}.deduped_bam": "{{ deduped_bam }}", "{{ project_name }}.deduped_bam": "{{ deduped_bam }}",
"{{ project_name }}.deduped_bam_index": "{{ deduped_bam_index }}", "{{ project_name }}.deduped_bam_index": "{{ deduped_bam_index }}",
"{{ project_name }}.fasta": "{{ fasta }}", "{{ project_name }}.fasta": "{{ fasta }}",

+ 1
- 1
tasks/PoN.wdl View File



File normal_bam File normal_bam
File normal_bam_index File normal_bam_index
String sample=basename(normal_bam, ".*")
String sample
String docker String docker
String cluster_config String cluster_config
String disk_size String disk_size

+ 4
- 3
workflow.wdl View File

workflow {{ project_name }} { workflow {{ project_name }} {
String SENTIEON_INSTALL_DIR String SENTIEON_INSTALL_DIR
String SENTIEON_LICENSE String SENTIEON_LICENSE
String panel_id
String sample_id


File deduped_bam File deduped_bam
File deduped_bam_index File deduped_bam_index
deduped_bam_index=deduped_bam_index, deduped_bam_index=deduped_bam_index,
db_mills=db_mills, db_mills=db_mills,
dbmills_dir=dbmills_dir, dbmills_dir=dbmills_dir,
sample=sample_id + '_tumor',
sample=sample_id,
docker=sentieon_docker, docker=sentieon_docker,
disk_size=disk_size, disk_size=disk_size,
cluster_config=cluster_config cluster_config=cluster_config
dbmills_dir=dbmills_dir, dbmills_dir=dbmills_dir,
dbsnp=dbsnp, dbsnp=dbsnp,
dbsnp_dir=dbsnp_dir, dbsnp_dir=dbsnp_dir,
sample=sample_id + '_tumor',
sample=sample_id,
docker=sentieon_docker, docker=sentieon_docker,
disk_size=disk_size, disk_size=disk_size,
cluster_config=cluster_config cluster_config=cluster_config
regions=regions, regions=regions,
normal_bam=BQSR.recaled_bam, normal_bam=BQSR.recaled_bam,
normal_bam_index=BQSR.recaled_bam_index, normal_bam_index=BQSR.recaled_bam_index,
sample=sample_id,
docker=sentieon_docker, docker=sentieon_docker,
disk_size=disk_size, disk_size=disk_size,
cluster_config=cluster_config cluster_config=cluster_config

Loading…
Cancel
Save