-
Notifications
You must be signed in to change notification settings - Fork 58
/
bam_to_trimmed_fastq_and_hisat_alignments.cwl
77 lines (76 loc) · 1.98 KB
/
bam_to_trimmed_fastq_and_hisat_alignments.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
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "bam to trimmed fastqs and HISAT alignments"
requirements:
- class: MultipleInputFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: InlineJavascriptRequirement
inputs:
bam:
type: File
adapters:
type: File
adapter_trim_end:
type: string
adapter_min_overlap:
type: int
max_uncalled:
type: int
min_readlength:
type: int
read_group_id:
type: string
read_group_fields:
type:
type: array
items: string
reference_index:
type: File
secondaryFiles: [".1.ht2", ".2.ht2", ".3.ht2", ".4.ht2", ".5.ht2", ".6.ht2", ".7.ht2", ".8.ht2"]
firststrand:
type: boolean?
secondstrand:
type: boolean?
outputs:
fastqs:
type: File[]
outputSource: trim_fastq/fastqs
aligned_bam:
type: File
outputSource: hisat2_align/aligned_bam
steps:
bam_to_fastq:
run: bam_to_fastq.cwl
in:
bam: bam
out:
[fastq1, fastq2]
trim_fastq:
run: trim_fastq.cwl
in:
reads1: bam_to_fastq/fastq1
reads2: bam_to_fastq/fastq2
adapters: adapters
adapter_trim_end: adapter_trim_end
adapter_min_overlap: adapter_min_overlap
max_uncalled: max_uncalled
min_readlength: min_readlength
out:
[fastqs]
hisat2_align:
run: hisat2_align.cwl
in:
reference_index: reference_index
fastq1:
source: trim_fastq/fastqs
valueFrom: $(self[0])
fastq2:
source: trim_fastq/fastqs
valueFrom: $(self[1])
read_group_id: read_group_id
read_group_fields: read_group_fields
firststrand: firststrand
secondstrand: secondstrand
out:
[aligned_bam]