/
wf_demultiplex_se.cwl
executable file
·85 lines (71 loc) · 1.83 KB
/
wf_demultiplex_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
#!/usr/bin/env cwltool
### This is kind of a worthless workflow, ###
### but to keep consistent with the paired-end ###
### pipeline, I'm keeping it here. ###
cwlVersion: v1.0
class: Workflow
requirements:
- class: StepInputExpressionRequirement
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement # TODO needed?
- class: MultipleInputFeatureRequirement
#hints:
# - class: ex:ScriptRequirement
# scriptlines:
# - "#!/bin/bash"
inputs:
dataset:
type: string
# randomer_length:
# type: string
# barcodesfasta:
# type: File
read:
type:
type: record
fields:
read1:
type: File
# barcodeids:
# type: string[]
name:
type: string
outputs:
### DEMUXED FILES ###
A_output_demuxed_read1:
type: File
outputSource: gzip_demux/gzipped
read_name:
type: string
outputSource: AB_demux/name
dataset_name:
type: string
outputSource: AB_demux/output_dataset
### TRIM/CUTADAPT PARAMS ###
steps:
###########################################################################
# Upstream
###########################################################################
AB_demux:
run: demux_se.cwl
in:
reads: read
dataset: dataset
out: [
demuxedAfwd,
output_demuxedsingleend_metrics,
output_dataset,
name
]
###########################################################################
# Downstream
###########################################################################
gzip_demux:
run: gzip.cwl
in:
input: AB_demux/demuxedAfwd
out:
- gzipped
doc: |
This workflow takes in single-end reads, and performs the following steps in order:
demux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol)