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Fixbug: pindel task name

master
YaqingLiu 3 anni fa
parent
commit
cd5f5ba56b
2 ha cambiato i file con 4 aggiunte e 4 eliminazioni
  1. +1
    -1
      tasks/pindel.wdl
  2. +3
    -3
      workflow.wdl

+ 1
- 1
tasks/pindel.wdl Vedi File

task pindel {
task Pindel {


String sample_id String sample_id
File bam File bam

+ 3
- 3
workflow.wdl Vedi File

import "./tasks/processSomatic.wdl" as processSomatic import "./tasks/processSomatic.wdl" as processSomatic
import "./tasks/somaticFilter.wdl" as somaticFilter import "./tasks/somaticFilter.wdl" as somaticFilter
import "./tasks/replaceRG.wdl" as replaceRG import "./tasks/replaceRG.wdl" as replaceRG
import "./tasks/pindel.wdl" as pindel
import "./tasks/Pindel.wdl" as Pindel
import "./tasks/ANNOVAR.wdl" as ANNOVAR import "./tasks/ANNOVAR.wdl" as ANNOVAR
import "./tasks/VEP.wdl" as VEP import "./tasks/VEP.wdl" as VEP


} }
if (pindel) { if (pindel) {
call pindel.pindel as pindel {
call Pindel.Pindel as Pindel {
input: input:
sample_id=sample_id + '.N', sample_id=sample_id + '.N',
bam=normal_BQSR.recaled_bam, bam=normal_BQSR.recaled_bam,
} }


if (pindel) { if (pindel) {
call pindel.pindel as pindel_fb {
call Pindel.Pindel as Pindel_fb {
input: input:
sample_id=sample_id + '.N', sample_id=sample_id + '.N',
bam=normal_BQSR_fb.recaled_bam, bam=normal_BQSR_fb.recaled_bam,

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