/
main.nf.test
212 lines (174 loc) · 8.08 KB
/
main.nf.test
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
212
nextflow_process {
name "Test Process FASTQC"
script "../main.nf"
process "FASTQC"
tag "modules"
tag "modules_nfcore"
tag "fastqc"
test("sarscov2 single-end [fastq]") {
when {
process {
"""
input[0] = Channel.of([
[ id: 'test', single_end:true ],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
])
"""
}
}
then {
assertAll (
{ assert process.success },
// NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it.
// looks like this: <div id="header_filename">Mon 2 Oct 2023<br/>test.gz</div>
// https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039
{ assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
{ assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
{ assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
{ assert snapshot(process.out.versions).match("fastqc_versions_single") }
)
}
}
test("sarscov2 paired-end [fastq]") {
when {
process {
"""
input[0] = Channel.of([
[id: 'test', single_end: false], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
])
"""
}
}
then {
assertAll (
{ assert process.success },
{ assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
{ assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
{ assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
{ assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
{ assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
{ assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
{ assert snapshot(process.out.versions).match("fastqc_versions_paired") }
)
}
}
test("sarscov2 interleaved [fastq]") {
when {
process {
"""
input[0] = Channel.of([
[id: 'test', single_end: false], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true)
])
"""
}
}
then {
assertAll (
{ assert process.success },
{ assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
{ assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
{ assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
{ assert snapshot(process.out.versions).match("fastqc_versions_interleaved") }
)
}
}
test("sarscov2 paired-end [bam]") {
when {
process {
"""
input[0] = Channel.of([
[id: 'test', single_end: false], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
])
"""
}
}
then {
assertAll (
{ assert process.success },
{ assert process.out.html[0][1] ==~ ".*/test_fastqc.html" },
{ assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" },
{ assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
{ assert snapshot(process.out.versions).match("fastqc_versions_bam") }
)
}
}
test("sarscov2 multiple [fastq]") {
when {
process {
"""
input[0] = Channel.of([
[id: 'test', single_end: false], // meta map
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ]
])
"""
}
}
then {
assertAll (
{ assert process.success },
{ assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" },
{ assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" },
{ assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" },
{ assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" },
{ assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" },
{ assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" },
{ assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" },
{ assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" },
{ assert path(process.out.html[0][1][0]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
{ assert path(process.out.html[0][1][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
{ assert path(process.out.html[0][1][2]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
{ assert path(process.out.html[0][1][3]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
{ assert snapshot(process.out.versions).match("fastqc_versions_multiple") }
)
}
}
test("sarscov2 custom_prefix") {
when {
process {
"""
input[0] = Channel.of([
[ id:'mysample', single_end:true ], // meta map
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
])
"""
}
}
then {
assertAll (
{ assert process.success },
{ assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" },
{ assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" },
{ assert path(process.out.html[0][1]).text.contains("<tr><td>File type</td><td>Conventional base calls</td></tr>") },
{ assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") }
)
}
}
test("sarscov2 single-end [fastq] - stub") {
options "-stub"
when {
process {
"""
input[0] = Channel.of([
[ id: 'test', single_end:true ],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ]
])
"""
}
}
then {
assertAll (
{ assert process.success },
{ assert snapshot(process.out.html.collect { file(it[1]).getName() } +
process.out.zip.collect { file(it[1]).getName() } +
process.out.versions ).match("fastqc_stub") }
)
}
}
}