-
Notifications
You must be signed in to change notification settings - Fork 7
/
TransDecoder-v5-wf-2steps.cwl
56 lines (49 loc) · 1.62 KB
/
TransDecoder-v5-wf-2steps.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
cwlVersion: v1.0
class: Workflow
label: TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed by TransDecoder.Predict (step2)
requirements:
- class: SchemaDefRequirement
types:
- $import: ../tools/TransDecoder/TransDecoder-v5-genetic_codes.yaml
inputs:
transcriptsFile:
type: File
# TODO: Resolve: Missing required 'format' for File at runtime
# format: edam:format_1929 # FASTA
singleBestOnly: boolean?
outputs:
peptide_sequences:
type: File
outputSource: predict_coding_regions/peptide_sequences
coding_regions:
type: File
outputSource: predict_coding_regions/coding_regions
gff3_output:
type: File
outputSource: predict_coding_regions/gff3_output
bed_output:
type: File
outputSource: predict_coding_regions/bed_output
steps:
extract_long_orfs:
label: Extracts the long open reading frames
run: ../tools/TransDecoder/TransDecoder.LongOrfs-v5.cwl
in:
transcriptsFile: transcriptsFile
out: [ workingDir ]
predict_coding_regions:
label: Predicts the likely coding regions
run: ../tools/TransDecoder/TransDecoder.Predict-v5.cwl
in:
transcriptsFile: transcriptsFile
longOpenReadingFrames: extract_long_orfs/workingDir
singleBestOnly: singleBestOnly
out: [ peptide_sequences, coding_regions, gff3_output, bed_output ]
$namespaces:
edam: http://edamontology.org/
s: http://schema.org/
$schemas:
- http://edamontology.org/EDAM_1.16.owl
- https://schema.org/docs/schema_org_rdfa.html
s:license: "https://www.apache.org/licenses/LICENSE-2.0"
s:copyrightHolder: "EMBL - European Bioinformatics Institute, 2018"