-
Notifications
You must be signed in to change notification settings - Fork 6
/
test-workflow.cwl
120 lines (105 loc) · 2.12 KB
/
test-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
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
#!/usr/bin/env cwl-runner
class: Workflow
id: test-workflow
label: test-workflow
cwlVersion: v1.0
$namespaces:
edam: 'http://edamontology.org/'
inputs:
fq1:
type: File
format: edam:format_1930
doc: FastQ file from next-generation sequencers
fq2:
type: File
format: edam:format_1930
doc: FastQ file from next-generation sequencers
fadir:
type: Directory
doc: directory containing FastA file and index
ref:
type: string
doc: name of reference (e.g., hs37d5)
steps:
qc1:
label: qc1
doc: Quality control for fastq file (fq1) before trimming
run: ../Tools/fastqc.cwl
in:
fastq: fq1
out: [qc]
qc2:
label: qc2
doc: Quality control for fastq file (fq2) before trimming
run: ../Tools/fastqc.cwl
in:
fastq: fq2
out: [qc]
trimPE:
label: trimPE
doc: adaptor trimming
run: ../Tools/trimmomaticPE.cwl
in:
fq1: fq1
fq2: fq2
out: [trimFq1P, trimFq2P]
qc1P:
label: qc1P
doc: Quality control for fastq file (fq1) after trimming
run: ../Tools/fastqc.cwl
in:
fastq: trimPE/trimFq1P
out: [qc]
qc2P:
label: qc2P
doc: Quality control for fastq file (fq2) after trimming
run: ../Tools/fastqc.cwl
in:
fastq: trimPE/trimFq2P
out: [qc]
map:
label: map
doc: Mapping onto a reference genome
run: ../Tools/bwa-mem-PE.cwl
in:
fadir: fadir
ref: ref
fq1: trimPE/trimFq1P
fq2: trimPE/trimFq2P
out: [sam]
sam2bam:
label: sam2bam
doc: Convert SAM to BAM
run: ../Tools/samtools-sam2bam.cwl
in:
sam: map/sam
out: [bam]
sort:
label: sort
doc: Sort BAM
run: ../Tools/samtools-sort.cwl
in:
bam: sam2bam/bam
out: [sorted-bam]
outputs:
oqc1:
type: File
outputSource: qc1/qc
oqc2:
type: File
outputSource: qc2/qc
oqc1P:
type: File
outputSource: qc1P/qc
oqc2P:
type: File
outputSource: qc2P/qc
sam:
type: File
outputSource: map/sam
bam:
type: File
outputSource: sam2bam/bam
osort:
type: File
outputSource: sort/sorted-bam