-
Notifications
You must be signed in to change notification settings - Fork 14
/
extract_readgroup_fastq_se.cwl
51 lines (44 loc) · 1.25 KB
/
extract_readgroup_fastq_se.cwl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
requirements:
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../../tools/readgroup.yml
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
inputs:
- id: readgroup_fastq_se_uuid
type: ../../tools/readgroup.yml#readgroup_fastq_se_uuid
- id: bioclient_config
type: File
outputs:
- id: output
type: ../../tools/readgroup.yml#readgroup_fastq_se_file
outputSource: emit_readgroup_fastq_se_file/output
steps:
- id: extract_fastq
run: ../../tools/bio_client_download.cwl
in:
- id: config-file
source: bioclient_config
- id: download_handle
source: readgroup_fastq_se_uuid
valueFrom: $(self.fastq_uuid)
- id: file_size
source: readgroup_fastq_se_uuid
valueFrom: $(self.fastq_file_size)
out:
- id: output
- id: emit_readgroup_fastq_se_file
run: ../../tools/emit_readgroup_fastq_se_file.cwl
in:
- id: fastq
source: extract_fastq/output
- id: readgroup_meta
source: readgroup_fastq_se_uuid
valueFrom: $(self.readgroup_meta)
out:
- id: output