-
Notifications
You must be signed in to change notification settings - Fork 19
/
abundance.workflow.cwl
71 lines (65 loc) · 1.78 KB
/
abundance.workflow.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
62
63
64
65
66
67
68
69
70
cwlVersion: v1.0
class: Workflow
label: abundance
doc: abundace profiles from annotated files, for protein and/or rna
requirements:
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
jobid: string
md5index: File
filterSims: File[]
expandSims: File[]
lcaAnns: File[]
clustMaps: File[]
coverage: File?
outputs:
md5ProfileOut:
type: File
outputSource: md5Profile/output
lcaProfileOut:
type: File
outputSource: lcaProfile/output
sourceStatsOut:
type: File
outputSource: sourceStats/output
steps:
md5Profile:
run: ../Tools/sims_abundance.tool.cwl
in:
input: filterSims
cluster: clustMaps
coverage: coverage
md5index: md5index
profileType:
valueFrom: md5
outName:
source: jobid
valueFrom: $(self).700.annotation.md5.abundance
out: [output]
lcaProfile:
run: ../Tools/sims_abundance.tool.cwl
in:
input: lcaAnns
cluster: clustMaps
coverage: coverage
profileType:
valueFrom: lca
outName:
source: jobid
valueFrom: $(self).700.annotation.lca.abundance
out: [output]
sourceStats:
run: ../Tools/sims_abundance.tool.cwl
in:
input: expandSims
cluster: clustMaps
coverage: coverage
profileType:
valueFrom: source
outName:
source: jobid
valueFrom: $(self).700.annotation.source.stats
out: [output]