/
peak-caller-MACE-SE.cwl
85 lines (77 loc) · 2.05 KB
/
peak-caller-MACE-SE.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
class: Workflow
cwlVersion: v1.0
label: MACE ChIP-exo peak caller workflow for single-end samples
doc: >-
This workflow execute peak caller and QC from ChIP-exo for single-end samples
using MACE
requirements:
InlineJavascriptRequirement: {}
StepInputExpressionRequirement: {}
SubworkflowFeatureRequirement: {}
ScatterFeatureRequirement: {}
inputs:
chrom_size: File
sorted_bam:
type: {"type": "array", "items": {"type": "array", "items": "File"}}
output_basename: string[]
genome_gtf: File
tss_size: int
norm_method: string
outputs:
annotated_bed:
outputSource: annotate_bed_gff/output
type: File[]
steps:
preprocessor:
run: ../../tools/mace/preprocessor.cwl
label: MACE-preprocessor
scatter: [i, o]
scatterMethod: dotproduct
in:
i: sorted_bam
o: output_basename
r: chrom_size
m: norm_method
out: [out_forward, out_reverse]
mace:
run: ../../tools/mace/mace.cwl
label: MACE
scatter: [f,r,o]
scatterMethod: dotproduct
in:
f: preprocessor/out_forward
o: output_basename
r: preprocessor/out_reverse
s: chrom_size
out: [border_cluster_out, border_out, border_pair_elite_out, border_pair_out]
bamscale_cov:
run: ../../tools/bamscale/bamscale-cov.cwl
label: BAMscale-cov
scatter: [bam, bed]
scatterMethod: dotproduct
in:
bam: sorted_bam
bed: mace/border_pair_out
n:
valueFrom: '${ return inputs.bed.nameroot;}'
out: [fpkm_out, library_out, raw_out, tpm_out]
annotate_bed_gff:
run: ../../tools/python/annotate_bed_gtf.cwl
label: annotate_bed
scatter: [bed, tpm]
scatterMethod: dotproduct
in:
gtf: genome_gtf
bed: mace/border_pair_out
tpm: bamscale_cov/tpm_out
tss_size: tss_size
out: [output]
$namespaces:
s: http://schema.org/
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0002-4108-5982
s:email: mailto:r78v10a07@gmail.com
s:name: Roberto Vera Alvarez
$schemas:
- https://schema.org/version/latest/schemaorg-current-http.rdf