Skip to content

Commit d6cfe40

Browse files
prototaxitesprototaxites
authored
Merge branch 'master' into gtdbtk
2 parents 6e2a4f9 + d0fcd22 commit d6cfe40

File tree

2 files changed

+83
-143
lines changed

2 files changed

+83
-143
lines changed

‎modules/nf-core/links/tests/main.nf.test‎

Lines changed: 13 additions & 53 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ nextflow_process {
77
tag "modules_nfcore"
88
tag "links"
99

10-
test("LINKS - LINKS test data") {
10+
test("LINKS - sarscov2 test data - contigs") {
1111
config './nextflow.config'
1212

1313
when {
@@ -18,11 +18,11 @@ nextflow_process {
1818
"""
1919
input[0] = [
2020
[ id:'test' ],
21-
file(params.modules_testdata_base_path + 'genomics/scaffolding/LINKS/contigs.fasta', checkIfExists: true),
21+
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
2222
]
2323
input[1] = [
2424
[ id:'test'],
25-
file(params.modules_testdata_base_path + 'genomics/scaffolding/LINKS/genome.fasta', checkIfExists: true),
25+
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
2626
]
2727
"""
2828
}
@@ -48,7 +48,7 @@ nextflow_process {
4848

4949
}
5050

51-
test("LINKS - longstitch test data 1") {
51+
test("LINKS - sarscov2 test data - scaffolds") {
5252
config './nextflow.config'
5353

5454
when {
@@ -59,11 +59,11 @@ nextflow_process {
5959
"""
6060
input[0] = [
6161
[ id:'test' ],
62-
file(params.modules_testdata_base_path + 'genomics/scaffolding/longstitch/test_scaffolds1.fa', checkIfExists: true),
62+
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/scaffolds.fasta', checkIfExists: true),
6363
]
6464
input[1] = [
6565
[ id:'test'],
66-
file(params.modules_testdata_base_path + 'genomics/scaffolding/longstitch/test_reads1.fa.gz', checkIfExists: true),
66+
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
6767
]
6868
"""
6969
}
@@ -74,53 +74,13 @@ nextflow_process {
7474
{ assert process.success },
7575
{ assert snapshot(
7676
file(process.out.log[0][1]).name,
77-
file(process.out.pairing_issues[0][1]).name,
78-
process.out.scaffolds_csv,
79-
process.out.scaffolds_fasta,
80-
process.out.bloom,
81-
file(process.out.scaffolds_graph[0][1]).name,
82-
file(process.out.assembly_correspondence[0][1]).name,
83-
file(process.out.tigpair_checkpoint[0][1]).name,
84-
process.out.versions
85-
).match()
86-
}
87-
)
88-
}
89-
90-
}
91-
test("LINKS - longstitch test data 2") {
92-
config './nextflow.config'
93-
94-
when {
95-
params {
96-
module_args = "-d 1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,12000,14000,16000,18000,20000"
97-
}
98-
process {
99-
"""
100-
input[0] = [
101-
[ id:'test' ],
102-
file(params.modules_testdata_base_path + 'genomics/scaffolding/longstitch/test_scaffolds2.fa', checkIfExists: true),
103-
]
104-
input[1] = [
105-
[ id:'test'],
106-
file(params.modules_testdata_base_path + 'genomics/scaffolding/longstitch/test_reads2.fa.gz', checkIfExists: true),
107-
]
108-
"""
109-
}
110-
}
111-
112-
then {
113-
assertAll(
114-
{ assert process.success },
115-
{ assert snapshot(
116-
file(process.out.log[0][1]).name,
117-
file(process.out.pairing_issues[0][1]).name,
77+
process.out.pairing_issues,
11878
process.out.scaffolds_csv,
11979
process.out.scaffolds_fasta,
12080
process.out.bloom,
12181
file(process.out.scaffolds_graph[0][1]).name,
122-
file(process.out.assembly_correspondence[0][1]).name,
123-
file(process.out.tigpair_checkpoint[0][1]).name,
82+
process.out.assembly_correspondence,
83+
process.out.tigpair_checkpoint,
12484
process.out.versions
12585
).match()
12686
}
@@ -140,12 +100,12 @@ nextflow_process {
140100
process {
141101
"""
142102
input[0] = [
143-
[ id:'test' ],
144-
file(params.modules_testdata_base_path + 'genomics/scaffolding/LINKS/contigs.fasta', checkIfExists: true),
103+
[ id:'test' ],
104+
file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
145105
]
146106
input[1] = [
147-
[ id:'test' ],
148-
file(params.modules_testdata_base_path + 'genomics/scaffolding/LINKS/genome.fasta', checkIfExists: true),
107+
[ id:'test'],
108+
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true),
149109
]
150110
"""
151111
}

‎modules/nf-core/links/tests/main.nf.test.snap‎

Lines changed: 70 additions & 90 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,66 @@
11
{
2+
"LINKS - sarscov2 test data - scaffolds": {
3+
"content": [
4+
"test.log",
5+
[
6+
[
7+
{
8+
"id": "test"
9+
},
10+
"test.pairing_issues:md5,d41d8cd98f00b204e9800998ecf8427e"
11+
]
12+
],
13+
[
14+
[
15+
{
16+
"id": "test"
17+
},
18+
"test.scaffolds:md5,095cc323b3af3a7873c8b80cf3736a1f"
19+
]
20+
],
21+
[
22+
[
23+
{
24+
"id": "test"
25+
},
26+
"test.scaffolds.fa:md5,b8c7938abbc3d2f9b5c3d709d43b4a60"
27+
]
28+
],
29+
[
30+
[
31+
{
32+
"id": "test"
33+
},
34+
"test.bloom:md5,23737e49d9a2f070b312da844201b494"
35+
]
36+
],
37+
"test.gv",
38+
[
39+
[
40+
{
41+
"id": "test"
42+
},
43+
"test.assembly_correspondence.tsv:md5,a65d30663dce705d382df52ab87ca8a4"
44+
]
45+
],
46+
[
47+
[
48+
{
49+
"id": "test"
50+
},
51+
"test.tigpair_checkpoint.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
52+
]
53+
],
54+
[
55+
"versions.yml:md5,f58863e433b849b1ef0dfc19cb57656b"
56+
]
57+
],
58+
"meta": {
59+
"nf-test": "0.9.2",
60+
"nextflow": "24.10.3"
61+
},
62+
"timestamp": "2025-04-25T14:13:53.050775593"
63+
},
264
"LINKS - stub": {
365
"content": [
466
{
@@ -176,121 +238,39 @@
176238
},
177239
"timestamp": "2025-04-11T11:49:53.947870525"
178240
},
179-
"LINKS - longstitch test data 1": {
180-
"content": [
181-
"test.log",
182-
"test.pairing_issues",
183-
[
184-
[
185-
{
186-
"id": "test"
187-
},
188-
"test.scaffolds:md5,e12db5e5e6a1b5e26d2b50b6256c960d"
189-
]
190-
],
191-
[
192-
[
193-
{
194-
"id": "test"
195-
},
196-
"test.scaffolds.fa:md5,afe56607a3d2c3b1e2d605bdf7ca545f"
197-
]
198-
],
199-
[
200-
[
201-
{
202-
"id": "test"
203-
},
204-
"test.bloom:md5,b912b31cfadaf81e722f5441ac639f60"
205-
]
206-
],
207-
"test.gv",
208-
"test.assembly_correspondence.tsv",
209-
"test.tigpair_checkpoint.tsv",
210-
[
211-
"versions.yml:md5,f58863e433b849b1ef0dfc19cb57656b"
212-
]
213-
],
214-
"meta": {
215-
"nf-test": "0.9.2",
216-
"nextflow": "24.10.3"
217-
},
218-
"timestamp": "2025-04-11T13:39:00.252899964"
219-
},
220-
"LINKS - longstitch test data 2": {
221-
"content": [
222-
"test.log",
223-
"test.pairing_issues",
224-
[
225-
[
226-
{
227-
"id": "test"
228-
},
229-
"test.scaffolds:md5,00a943691b987adebe0ab40efced9c7e"
230-
]
231-
],
232-
[
233-
[
234-
{
235-
"id": "test"
236-
},
237-
"test.scaffolds.fa:md5,ed43c629e8d440e3cf6fb8b21742557c"
238-
]
239-
],
240-
[
241-
[
242-
{
243-
"id": "test"
244-
},
245-
"test.bloom:md5,695262bb4beda52665d2f7ec476a4e7b"
246-
]
247-
],
248-
"test.gv",
249-
"test.assembly_correspondence.tsv",
250-
"test.tigpair_checkpoint.tsv",
251-
[
252-
"versions.yml:md5,f58863e433b849b1ef0dfc19cb57656b"
253-
]
254-
],
255-
"meta": {
256-
"nf-test": "0.9.2",
257-
"nextflow": "24.10.3"
258-
},
259-
"timestamp": "2025-04-11T13:39:36.483298325"
260-
},
261-
"LINKS - LINKS test data": {
241+
"LINKS - sarscov2 test data - contigs": {
262242
"content": [
263243
"test.log",
264244
[
265245
[
266246
{
267247
"id": "test"
268248
},
269-
"test.pairing_issues:md5,eb8b04b4ec170a319b40d2ee16a5cf96"
249+
"test.pairing_issues:md5,d41d8cd98f00b204e9800998ecf8427e"
270250
]
271251
],
272252
[
273253
[
274254
{
275255
"id": "test"
276256
},
277-
"test.scaffolds:md5,afe5339405b830e97095058080550064"
257+
"test.scaffolds:md5,41c129edd1e66140fcfb7efce81197ad"
278258
]
279259
],
280260
[
281261
[
282262
{
283263
"id": "test"
284264
},
285-
"test.scaffolds.fa:md5,4aa442ee4b05e1608daf7b5b033a4203"
265+
"test.scaffolds.fa:md5,8abc4f609d0ad415f900b0046b38a72b"
286266
]
287267
],
288268
[
289269
[
290270
{
291271
"id": "test"
292272
},
293-
"test.bloom:md5,96f54f577d1c589251ea0cfe624b898d"
273+
"test.bloom:md5,23737e49d9a2f070b312da844201b494"
294274
]
295275
],
296276
"test.gv",
@@ -299,15 +279,15 @@
299279
{
300280
"id": "test"
301281
},
302-
"test.assembly_correspondence.tsv:md5,0efc40db474ba8d5b334ad48add4bd9d"
282+
"test.assembly_correspondence.tsv:md5,b36e951b0a1bb4b1c1ccd50925392e3d"
303283
]
304284
],
305285
[
306286
[
307287
{
308288
"id": "test"
309289
},
310-
"test.tigpair_checkpoint.tsv:md5,9208c8fe686b5989eaec1485a74cf44e"
290+
"test.tigpair_checkpoint.tsv:md5,168f2075f524a86216118c7230ad65e9"
311291
]
312292
],
313293
[
@@ -318,6 +298,6 @@
318298
"nf-test": "0.9.2",
319299
"nextflow": "24.10.3"
320300
},
321-
"timestamp": "2025-04-11T11:30:01.790074303"
301+
"timestamp": "2025-04-25T14:07:49.212617595"
322302
}
323303
}

0 commit comments

Comments
 (0)