/
bowtie-index.cwl
121 lines (94 loc) · 3.03 KB
/
bowtie-index.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
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
'sd:metadata':
- "../metadata/indices-header.cwl"
inputs:
genome:
type: string
label: "Genome type"
doc: "Genome type, such as mm10, hg19, hg38, etc"
fasta_file:
type: File
format: "http://edamontology.org/format_1929"
label: "Reference genome FASTA file"
doc: "Reference genome FASTA file. Includes all chromosomes"
outputs:
indices_folder:
type: Directory
label: "Bowtie indices"
doc: "Bowtie generated indices folder"
outputSource: bowtie_build/indices_folder
stdout_log:
type: File
label: "Bowtie stdout log"
doc: "Bowtie generated stdout log"
outputSource: bowtie_build/stdout_log
stderr_log:
type: File
label: "Bowtie stderr log"
doc: "Bowtie generated stderr log"
outputSource: bowtie_build/stderr_log
steps:
bowtie_build:
run: ../tools/bowtie-build.cwl
in:
fasta_file: fasta_file
index_base_name: genome
out:
- indices_folder
- stdout_log
- stderr_log
$namespaces:
s: http://schema.org/
$schemas:
- https://github.com/schemaorg/schemaorg/raw/main/data/releases/11.01/schemaorg-current-http.rdf
s:name: "Build Bowtie indices"
label: "Build Bowtie indices"
s:alternateName: "Build Bowtie indices"
s:downloadUrl: https://raw.githubusercontent.com/datirium/workflows/master/dummy/bowtie-index.cwl
s:codeRepository: https://github.com/datirium/workflows
s:license: http://www.apache.org/licenses/LICENSE-2.0
s:isPartOf:
class: s:CreativeWork
s:name: Common Workflow Language
s:url: http://commonwl.org/
s:creator:
- class: s:Organization
s:legalName: "Cincinnati Children's Hospital Medical Center"
s:location:
- class: s:PostalAddress
s:addressCountry: "USA"
s:addressLocality: "Cincinnati"
s:addressRegion: "OH"
s:postalCode: "45229"
s:streetAddress: "3333 Burnet Ave"
s:telephone: "+1(513)636-4200"
s:logo: "https://www.cincinnatichildrens.org/-/media/cincinnati%20childrens/global%20shared/childrens-logo-new.png"
s:department:
- class: s:Organization
s:legalName: "Allergy and Immunology"
s:department:
- class: s:Organization
s:legalName: "Barski Research Lab"
s:member:
- class: s:Person
s:name: Michael Kotliar
s:email: mailto:michael.kotliar@cchmc.org
s:sameAs:
- id: http://orcid.org/0000-0002-6486-3898
- class: s:Person
s:name: Andrey Kartashov
s:email: mailto:Andrey.Kartashov@cchmc.org
s:sameAs:
- id: http://orcid.org/0000-0001-9102-5681
# doc:
# $include: ../descriptions/bowtie-index.md
doc: |
Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference
genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that
corresponds to the input genome