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cwlVersion: v1.0
class: Workflow
# Taken from: https://github.com/zhangb1/gdc-workflow-cwl-v1/blob/master/fastq2cram-workflow.cwl
id: fastq2cram
label: fastq2cram
inputs:
- id: reference
type: File?
'sbg:x': 78.37765892459501
'sbg:y': -136.8996442549593
- id: output_bam
type: string?
'sbg:exposed': true
- id: output_cram
type: string?
'sbg:exposed': true
- id: read_group
type: string?
'sbg:exposed': true
- id: input2
type: File?
'sbg:x': -133.16793823242188
'sbg:y': -19.701574325561523
- id: input1
type: File?
'sbg:x': -247.71234130859375
'sbg:y': 134.93338012695312
outputs:
- id: output
outputSource:
- bam2cram/output
type: File?
'sbg:x': 867.6041259765625
'sbg:y': 37.68014144897461
- id: output_1
outputSource:
- picard_markduplicates/output
type: File?
'sbg:x': 703.6041259765625
'sbg:y': 199.79299926757812
steps:
- id: picard_bam_sort
in:
- id: input_bam
source:
- bwa_mem/output_1
- id: output_bam
default: sample.sort.bam
out:
- id: output
run: /Users/zhangb1/Documents/Tools/CWL.V1/GDC/tools/picard-bam-sort.cwl
label: picard-bam-sort
'sbg:x': 330.38558620876734
'sbg:y': 86.0821516248915
- id: picard_markduplicates
in:
- id: input_bam
source:
- picard_bam_sort/output
- id: output_bam
source:
- output_bam
out:
- id: output
run: /Users/zhangb1/Documents/Tools/CWL.V1/GDC/tools/picard-markduplicates.cwl
label: picard-MarkDuplicates
'sbg:x': 529.472669813368
'sbg:y': 117.65579393174913
- id: bam2cram
in:
- id: input_bam
source:
- picard_markduplicates/output
- id: reference
source:
- reference
- id: output_cram
source:
- output_cram
out:
- id: output
run: /Users/zhangb1/Documents/Tools/CWL.V1/GDC/tools/bam2cram.cwl
label: bam2cram
'sbg:x': 664.7517020756547
'sbg:y': 44.40993377363144
- id: bwa_mem
in:
- id: read_group
source:
- read_group
- id: reference
source:
- reference
- id: input1
source:
- input1
- id: output
default: sample.bam
- id: input2
source:
- input2
out:
- id: output_1
run: /Users/zhangb1/Documents/Tools/CWL.V1/GDC/tools/bwa-mem.cwl
label: bwa-mem
'sbg:x': 180.05976485693787
'sbg:y': 45.29557418823242
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