forked from Duke-GCB/GGR-cwl
/
01-qc-pe.cwl
211 lines (211 loc) · 6.14 KB
/
01-qc-pe.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
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
doc: 'ATAC-seq 01 QC - reads: PE'
requirements:
- class: ScatterFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
inputs:
input_read1_fastq_files:
doc: Input read1 fastq files
type: File[]
input_read2_fastq_files:
doc: Input read2 fastq files
type: File[]
default_adapters_file:
doc: Adapters file
type: File
nthreads:
doc: Number of threads.
type: int
steps:
extract_basename_read1:
run: ../utils/basename.cwl
scatter: file_path
in:
file_path:
source: input_read1_fastq_files
valueFrom: $(self.basename)
sep:
valueFrom: '(\.fastq.gz|\.fastq)'
do_not_escape_sep:
valueFrom: ${return true}
out:
- basename
count_raw_reads_read1:
run: ../utils/count-fastq-reads.cwl
scatterMethod: dotproduct
scatter:
- input_fastq_file
- input_basename
in:
input_basename: extract_basename_read1/basename
input_fastq_file: input_read1_fastq_files
out:
- output_read_count
fastqc_read1:
run: ../qc/fastqc.cwl
scatter: input_fastq_file
in:
threads: nthreads
input_fastq_file: input_read1_fastq_files
out:
- output_qc_report_file
extract_fastqc_data_read1:
run: ../qc/extract_fastqc_data.cwl
scatterMethod: dotproduct
scatter:
- input_qc_report_file
- input_basename
in:
input_basename: extract_basename_read1/basename
input_qc_report_file: fastqc_read1/output_qc_report_file
out:
- output_fastqc_data_file
overrepresented_sequence_extract_read1:
run: ../qc/overrepresented_sequence_extract.cwl
scatterMethod: dotproduct
scatter:
- input_fastqc_data
- input_basename
in:
input_fastqc_data: extract_fastqc_data_read1/output_fastqc_data_file
input_basename: extract_basename_read1/basename
default_adapters_file: default_adapters_file
out:
- output_custom_adapters
compare_read_counts_read1:
run: ../qc/diff.cwl
scatterMethod: dotproduct
scatter:
- file1
- file2
in:
file2: count_fastqc_reads_read1/output_fastqc_read_count
file1: count_raw_reads_read1/output_read_count
out:
- result
count_fastqc_reads_read1:
run: ../qc/count-fastqc-reads.cwl
scatterMethod: dotproduct
scatter:
- input_fastqc_data
- input_basename
in:
input_fastqc_data: extract_fastqc_data_read1/output_fastqc_data_file
input_basename: extract_basename_read1/basename
out:
- output_fastqc_read_count
extract_basename_read2:
run: ../utils/basename.cwl
scatter: file_path
in:
file_path:
source: input_read2_fastq_files
valueFrom: $(self.basename)
sep:
valueFrom: '(\.fastq.gz|\.fastq)'
do_not_escape_sep:
valueFrom: ${return true}
out:
- basename
count_raw_reads_read2:
run: ../utils/count-fastq-reads.cwl
scatterMethod: dotproduct
scatter:
- input_fastq_file
- input_basename
in:
input_basename: extract_basename_read2/basename
input_fastq_file: input_read2_fastq_files
out:
- output_read_count
fastqc_read2:
run: ../qc/fastqc.cwl
scatter: input_fastq_file
in:
threads: nthreads
input_fastq_file: input_read2_fastq_files
out:
- output_qc_report_file
extract_fastqc_data_read2:
run: ../qc/extract_fastqc_data.cwl
scatterMethod: dotproduct
scatter:
- input_qc_report_file
- input_basename
in:
input_basename: extract_basename_read2/basename
input_qc_report_file: fastqc_read2/output_qc_report_file
out:
- output_fastqc_data_file
overrepresented_sequence_extract_read2:
run: ../qc/overrepresented_sequence_extract.cwl
scatterMethod: dotproduct
scatter:
- input_fastqc_data
- input_basename
in:
input_fastqc_data: extract_fastqc_data_read2/output_fastqc_data_file
input_basename: extract_basename_read2/basename
default_adapters_file: default_adapters_file
out:
- output_custom_adapters
compare_read_counts_read2:
run: ../qc/diff.cwl
scatterMethod: dotproduct
scatter:
- file1
- file2
in:
file2: count_fastqc_reads_read2/output_fastqc_read_count
file1: count_raw_reads_read2/output_read_count
out:
- result
count_fastqc_reads_read2:
run: ../qc/count-fastqc-reads.cwl
scatterMethod: dotproduct
scatter:
- input_fastqc_data
- input_basename
in:
input_fastqc_data: extract_fastqc_data_read2/output_fastqc_data_file
input_basename: extract_basename_read2/basename
out:
- output_fastqc_read_count
outputs:
output_fastqc_data_files_read1:
doc: FastQC data files for paired_read1
type: File[]
outputSource: extract_fastqc_data_read1/output_fastqc_data_file
output_fastqc_report_files_read1:
doc: FastQC reports in zip format for paired_read1
type: File[]
outputSource: fastqc_read1/output_qc_report_file
output_custom_adapters_read1:
outputSource: overrepresented_sequence_extract_read1/output_custom_adapters
type: File[]
output_count_raw_reads_read1:
outputSource: count_raw_reads_read1/output_read_count
type: File[]
output_diff_counts_read1:
outputSource: compare_read_counts_read1/result
type: File[]
output_fastqc_data_files_read2:
doc: FastQC data files for paired_read2
type: File[]
outputSource: extract_fastqc_data_read2/output_fastqc_data_file
output_fastqc_report_files_read2:
doc: FastQC reports in zip format for paired_read2
type: File[]
outputSource: fastqc_read2/output_qc_report_file
output_custom_adapters_read2:
outputSource: overrepresented_sequence_extract_read2/output_custom_adapters
type: File[]
output_count_raw_reads_read2:
outputSource: count_raw_reads_read2/output_read_count
type: File[]
output_diff_counts_read2:
outputSource: compare_read_counts_read2/result
type: File[]