/
fastq_clean_se.cwl
61 lines (53 loc) · 1.32 KB
/
fastq_clean_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
52
53
54
55
56
57
58
59
60
61
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
requirements:
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
- class: SchemaDefRequirement
types:
- $import: ../../tools/readgroup.yml
class: Workflow
inputs:
- id: input
type: ../../tools/readgroup.yml#readgroup_fastq_se_file
- id: job_uuid
type: string
outputs:
- id: output
type: ../../tools/readgroup.yml#readgroup_fastq_se_file
outputSource: emit_readgroup_fastq_se_file/output
- id: sqlite
type: File
outputSource: json_to_sqlite/sqlite
steps:
- id: fastq_cleaner_se
run: ../../tools/fastq_cleaner_se.cwl
in:
- id: fastq
source: input
valueFrom: $(self.fastq)
out:
- id: cleaned_fastq
- id: result_json
- id: emit_readgroup_fastq_se_file
run: ../../tools/emit_readgroup_fastq_se_file.cwl
in:
- id: fastq
source: fastq_cleaner_se/cleaned_fastq
- id: readgroup_meta
source: input
valueFrom: $(self.readgroup_meta)
out:
- id: output
- id: json_to_sqlite
run: ../../tools/json_to_sqlite.cwl
in:
- id: input_json
source: fastq_cleaner_se/result_json
- id: job_uuid
source: job_uuid
- id: table_name
valueFrom: "fastq_cleaner_se"
out:
- id: sqlite
- id: log