-
Notifications
You must be signed in to change notification settings - Fork 3
/
fastqPE2bam.cwl
103 lines (87 loc) · 1.88 KB
/
fastqPE2bam.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
#!/usr/bin/env cwl-runner
class: Workflow
id: fastqPE2bam
label: fastqPE2bam
cwlVersion: v1.0
$namespaces:
edam: 'http://edamontology.org/'
inputs:
reference:
type: File
format: edam:format_1929
doc: FastA file for reference genome
secondaryFiles:
- .amb
- .ann
- .bwt
- .pac
- .sa
RG_ID:
type: string
doc: Read group identifier (ID) in RG line
RG_PL:
type: string
doc: Platform/technology used to produce the read (PL) in RG line
RG_PU:
type: string
doc: Platform Unit (PU) in RG line
RG_LB:
type: string
doc: DNA preparation library identifier (LB) in RG line
RG_SM:
type: string
doc: Sample (SM) identifier in RG line
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
nthreads:
type: int
doc: number of cpu cores to be used
outprefix:
type: string
doc: Output prefix name
steps:
bwa_mem_PE:
label: bwa_mem_PE
doc: Mapping onto reference using BWA MEM
run: ../Tools/bwa-mem-PE.cwl
in:
reference: reference
RG_ID: RG_ID
RG_PL: RG_PL
RG_PU: RG_PU
RG_LB: RG_LB
RG_SM: RG_SM
fq1: fq1
fq2: fq2
nthreads: nthreads
outprefix: outprefix
out: [sam, log]
picard_SortSam:
label: picard_SortSam
doc: Sort sam file and save as bam file
run: ../Tools/picard-SortSam.cwl
in:
sam: bwa_mem_PE/sam
outprefix: outprefix
out: [bam, log]
outputs:
sam:
type: File
format: edam:format_2573
outputSource: bwa_mem_PE/sam
sam_log:
type: File
outputSource: bwa_mem_PE/log
bam:
type: File
format: edam:format_2572
outputSource: picard_SortSam/bam
bam_log:
type: File
outputSource: picard_SortSam/log