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LouisLeNezetLouisLeNezet
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Update test
1 parent 42425dd commit cd6b0ec

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Lines changed: 115 additions & 81 deletions

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‎subworkflows/nf-core/fastq_fetch_clean_hostile/main.nf‎

Lines changed: 3 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,6 @@ workflow FASTQ_FETCH_CLEAN_HOSTILE {
99
index_name // val (optional)
1010

1111
main:
12-
ch_versions = channel.empty()
1312

1413
if (!index_name && !ch_reference) {
1514
error "Provide either the reference index name for HOSTILE_FETCH or an existing reference path for HOSTILE_CLEAN."
@@ -22,18 +21,15 @@ workflow FASTQ_FETCH_CLEAN_HOSTILE {
2221
if (index_name) {
2322
HOSTILE_FETCH( index_name )
2423
out_reference = HOSTILE_FETCH.out.reference
25-
ch_versions = ch_versions.mix(HOSTILE_FETCH.out.versions.first())
2624
}
2725
else {
2826
out_reference = ch_reference
2927
}
3028

3129
HOSTILE_CLEAN( ch_reads, out_reference )
32-
ch_versions = ch_versions.mix(HOSTILE_CLEAN.out.versions.first())
3330

3431
emit:
35-
reference = out_reference // channel: [ val(reference_name), path(reference_dir) ]
36-
fastq = HOSTILE_CLEAN.out.fastq // channel: [ val(meta), [ *.fastq.gz ] ]
37-
json = HOSTILE_CLEAN.out.json // channel: [ val(meta), [ *.json ] ]
38-
versions = ch_versions // channel: [ versions.yml ]
32+
reference = out_reference // channel: [ val(reference_name), path(reference_dir) ]
33+
fastq = HOSTILE_CLEAN.out.fastq // channel: [ val(meta), [ *.fastq.gz ] ]
34+
json = HOSTILE_CLEAN.out.json // channel: [ val(meta), [ *.json ] ]
3935
}

‎subworkflows/nf-core/fastq_fetch_clean_hostile/meta.yml‎

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -51,10 +51,6 @@ output:
5151
Channel containing sample metadata and Hostile cleaning log in JSON format.
5252
Structure: [ val(meta), path(*.json) ]
5353
pattern: "*.json"
54-
- versions:
55-
type: file
56-
description: File containing software versions
57-
pattern: "versions.yml"
5854
authors:
5955
- "@maia-munteanu"
6056
maintainers:

‎subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test‎

Lines changed: 3 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -44,10 +44,7 @@ nextflow_workflow {
4444
then {
4545
assertAll(
4646
{ assert workflow.success },
47-
{ assert snapshot(
48-
workflow.out.fastq,
49-
workflow.out.versions.collect{ path(it).yaml }.unique()
50-
).match() }
47+
{ assert snapshot(sanitizeOutput(workflow.out, unstableKeys: ["json"])).match() }
5148
)
5249
}
5350
}
@@ -72,10 +69,7 @@ nextflow_workflow {
7269
then {
7370
assertAll(
7471
{ assert workflow.success },
75-
{ assert snapshot(
76-
workflow.out.fastq,
77-
workflow.out.versions.collect{ path(it).yaml }.unique()
78-
).match() }
72+
{ assert snapshot(sanitizeOutput(workflow.out, unstableKeys: ["json"])).match() }
7973
)
8074
}
8175
}
@@ -100,10 +94,7 @@ nextflow_workflow {
10094
then {
10195
assertAll(
10296
{ assert workflow.success },
103-
{ assert snapshot(
104-
workflow.out.fastq,
105-
workflow.out.versions.collect{ path(it).yaml }.unique()
106-
).match() }
97+
{ assert snapshot(sanitizeOutput(workflow.out)).match() }
10798
)
10899
}
109100
}

‎subworkflows/nf-core/fastq_fetch_clean_hostile/tests/main.nf.test.snap‎

Lines changed: 109 additions & 58 deletions
Original file line numberDiff line numberDiff line change
@@ -1,80 +1,131 @@
11
{
22
"fastq - single-end - with reference - stub": {
33
"content": [
4-
[
5-
[
6-
{
7-
"id": "test_single",
8-
"single_end": true
9-
},
10-
"test_single.clean_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
4+
{
5+
"fastq": [
6+
[
7+
{
8+
"id": "test_single",
9+
"single_end": true
10+
},
11+
"test_single.clean_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
12+
]
13+
],
14+
"json": [
15+
[
16+
{
17+
"id": "test_single",
18+
"single_end": true
19+
},
20+
"test_single.json:md5,d41d8cd98f00b204e9800998ecf8427e"
21+
]
22+
],
23+
"reference": [
24+
[
25+
"genome",
26+
[
27+
"genome.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
28+
"genome.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
29+
"genome.3.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
30+
"genome.4.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
31+
"genome.rev.1.bt2:md5,d41d8cd98f00b204e9800998ecf8427e",
32+
"genome.rev.2.bt2:md5,d41d8cd98f00b204e9800998ecf8427e"
33+
]
34+
]
1135
]
12-
],
13-
[
14-
{
15-
"FASTQ_FETCH_CLEAN_HOSTILE:HOSTILE_CLEAN": {
16-
"hostile": "2.0.2"
17-
}
18-
}
19-
]
36+
}
2037
],
38+
"timestamp": "2026-05-26T14:30:20.029664659",
2139
"meta": {
22-
"nf-test": "0.9.3",
23-
"nextflow": "25.10.0"
24-
},
25-
"timestamp": "2025-11-10T09:37:58.736062"
40+
"nf-test": "0.9.5",
41+
"nextflow": "26.04.0"
42+
}
2643
},
2744
"fastq - single-end - with reference": {
2845
"content": [
29-
[
30-
[
31-
{
32-
"id": "test_single",
33-
"single_end": true
34-
},
35-
"test_1.clean.fastq.gz:md5,9224ada21765cb3ad5fc05f40df78f17"
46+
{
47+
"fastq": [
48+
[
49+
{
50+
"id": "test_single",
51+
"single_end": true
52+
},
53+
"test_1.clean.fastq.gz:md5,9224ada21765cb3ad5fc05f40df78f17"
54+
]
55+
],
56+
"json": [
57+
[
58+
{
59+
"id": "test_single",
60+
"single_end": true
61+
},
62+
"test_single.json"
63+
]
64+
],
65+
"reference": [
66+
[
67+
"genome",
68+
[
69+
"genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
70+
"genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
71+
"genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
72+
"genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
73+
"genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
74+
"genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
75+
]
76+
]
3677
]
37-
],
38-
[
39-
{
40-
"FASTQ_FETCH_CLEAN_HOSTILE:HOSTILE_CLEAN": {
41-
"hostile": "2.0.2"
42-
}
43-
}
44-
]
78+
}
4579
],
80+
"timestamp": "2026-05-26T14:43:39.771257929",
4681
"meta": {
47-
"nf-test": "0.9.3",
48-
"nextflow": "25.10.0"
49-
},
50-
"timestamp": "2025-11-10T09:37:39.689986"
82+
"nf-test": "0.9.5",
83+
"nextflow": "26.04.0"
84+
}
5185
},
5286
"fastq - paired-end - with reference": {
5387
"content": [
54-
[
55-
[
56-
{
57-
"id": "test_paired",
58-
"single_end": false
59-
},
88+
{
89+
"fastq": [
90+
[
91+
{
92+
"id": "test_paired",
93+
"single_end": false
94+
},
95+
[
96+
"test_1.clean_1.fastq.gz:md5,6de988b85909e6529bad0022703bcab2",
97+
"test_2.clean_2.fastq.gz:md5,539acd65e93bf16a5ace7d6034e704c7"
98+
]
99+
]
100+
],
101+
"json": [
102+
[
103+
{
104+
"id": "test_paired",
105+
"single_end": false
106+
},
107+
"test_paired.json"
108+
]
109+
],
110+
"reference": [
60111
[
61-
"test_1.clean_1.fastq.gz:md5,6de988b85909e6529bad0022703bcab2",
62-
"test_2.clean_2.fastq.gz:md5,539acd65e93bf16a5ace7d6034e704c7"
112+
"genome",
113+
[
114+
"genome.1.bt2:md5,cbe3d0bbea55bc57c99b4bfa25b5fbdf",
115+
"genome.2.bt2:md5,47b153cd1319abc88dda532462651fcf",
116+
"genome.3.bt2:md5,4ed93abba181d8dfab2e303e33114777",
117+
"genome.4.bt2:md5,c25be5f8b0378abf7a58c8a880b87626",
118+
"genome.rev.1.bt2:md5,52be6950579598a990570fbcf5372184",
119+
"genome.rev.2.bt2:md5,e3b4ef343dea4dd571642010a7d09597"
120+
]
63121
]
64122
]
65-
],
66-
[
67-
{
68-
"FASTQ_FETCH_CLEAN_HOSTILE:HOSTILE_CLEAN": {
69-
"hostile": "2.0.2"
70-
}
71-
}
72-
]
123+
}
73124
],
125+
"timestamp": "2026-05-26T14:44:03.047395234",
74126
"meta": {
75-
"nf-test": "0.9.3",
76-
"nextflow": "25.10.0"
77-
},
78-
"timestamp": "2025-11-10T09:37:51.783759"
127+
"nf-test": "0.9.5",
128+
"nextflow": "26.04.0"
129+
}
79130
}
80131
}

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