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update tests
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2 files changed

+60
-31
lines changed

2 files changed

+60
-31
lines changed

‎nf-tests/default.nf.test‎

Lines changed: 19 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -40,7 +40,19 @@ nextflow_pipeline {
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sorted_rows.each { row ->
4141
lines.add(header.collect { col -> row[col] ?: '' }.join('\t'))
4242
}
43-
return [name: file.name, md5: listToMD5(lines)]
43+
return [name: file.name, md5: listToMD5(lines), lineCount: lines.size()]
44+
}
45+
def fixed_line_number_files = getAllFilesFromDir(params.output_folder, include:['RootHOGs.tsv', 'OrthologousGroups.tsv', 'orthologs.tsv.gz', "FastOMA_HOGs.orthoxml", 'hogmap/*.hogmap']).collect { file ->
46+
def line_count
47+
if (file.name.endsWith('.gz')) {
48+
// Use try-with-resources for proper cleanup
49+
new java.util.zip.GZIPInputStream(file.newInputStream()).withCloseable { gzipStream ->
50+
line_count = gzipStream.readLines().size()
51+
}
52+
} else {
53+
line_count = file.readLines().size()
54+
}
55+
return [name: file.name, lineCount: line_count]
4456
}
4557

4658
assertAll(
@@ -53,7 +65,12 @@ nextflow_pipeline {
5365
// All files with stable contents
5466
stable_path,
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// List of all files with timestamps filtered out
56-
timestamp_files
68+
// does not yet work, as hogmap files have percision issues
69+
// and FastOMA_HOGs is not completely deterministic
70+
// timestamp_files
71+
72+
// files with fixed number of lines
73+
fixed_line_number_files
5774
).match() }
5875
)
5976
}

‎nf-tests/default.nf.test.snap‎

Lines changed: 41 additions & 29 deletions
Original file line numberDiff line numberDiff line change
@@ -44,56 +44,68 @@
4444
"stats"
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],
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[
47-
"OG_0000001.fa.gz:md5,0d66f05814d8ae19cfc92e9c524732ec",
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"OG_0000002.fa.gz:md5,ef9c8f91804962843307a71b115398ca",
49-
"OG_0000003.fa.gz:md5,a9a53b274a2ee456e8f42f29f7cdd041",
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"OG_0000004.fa.gz:md5,ae11efbff2957ec2fd5f26e7043f1044",
51-
"OG_0000005.fa.gz:md5,9747e7267109929d902a0cd921b9a4a9",
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"OG_0000006.fa.gz:md5,cc5b8cfcb48b384c870b39c36182add9",
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"OG_0000007.fa.gz:md5,ad8c0d95094dd8817fe510e752ae7e89",
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"OG_0000008.fa.gz:md5,b5de472745972a17a29bdf2f0129d8fa",
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"OG_0000009.fa.gz:md5,4bad2b524cb84aecdf19b0f93ea8534e",
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"OG_0000010.fa.gz:md5,d9b8763576656b3e747d5a87de6f74b8",
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"OG_0000011.fa.gz:md5,443fab9c4961ebfb8187165be27a9577",
58-
"OG_0000012.fa.gz:md5,e4b128f477155cd74ff10528d7adc09f",
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"HOG0000001.fa.gz:md5,0d66f05814d8ae19cfc92e9c524732ec",
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"HOG0000002.fa.gz:md5,ef9c8f91804962843307a71b115398ca",
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"HOG0000003.fa.gz:md5,a9a53b274a2ee456e8f42f29f7cdd041",
62-
"HOG0000004.fa.gz:md5,ae11efbff2957ec2fd5f26e7043f1044",
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"HOG0000005.fa.gz:md5,9747e7267109929d902a0cd921b9a4a9",
64-
"HOG0000006.fa.gz:md5,cc5b8cfcb48b384c870b39c36182add9",
65-
"HOG0000007.fa.gz:md5,ad8c0d95094dd8817fe510e752ae7e89",
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"HOG0000008.fa.gz:md5,b5de472745972a17a29bdf2f0129d8fa",
67-
"HOG0000009.fa.gz:md5,4bad2b524cb84aecdf19b0f93ea8534e",
68-
"HOG0000010.fa.gz:md5,d9b8763576656b3e747d5a87de6f74b8",
69-
"HOG0000011.fa.gz:md5,443fab9c4961ebfb8187165be27a9577",
70-
"HOG0000012.fa.gz:md5,e4b128f477155cd74ff10528d7adc09f",
47+
"OG_0000001.fa.gz:md5,4f2f37d12e4ff633a9b94e33a88e455a",
48+
"OG_0000002.fa.gz:md5,adfcb601ad79f42045f9af52265da97a",
49+
"OG_0000003.fa.gz:md5,1c0dd6e5d568daa80ffaf2181285bb11",
50+
"OG_0000004.fa.gz:md5,398d13abab8188b12b2974f435ada83b",
51+
"OG_0000005.fa.gz:md5,d84212a81ba4c7617b3fcc5a6fe19df3",
52+
"OG_0000006.fa.gz:md5,e16e7a970c10b0da63739fee1ce9fd13",
53+
"OG_0000007.fa.gz:md5,44be5719ddf0eead5eecc1efcb2020bb",
54+
"OG_0000008.fa.gz:md5,2fe75a29eeb184440dae58b0e293fc06",
55+
"OG_0000009.fa.gz:md5,f74a157bc1af82adb3a9b160d6de137a",
56+
"OG_0000010.fa.gz:md5,cd22e8c78937ba7ba1ef9224fe04732d",
57+
"OG_0000011.fa.gz:md5,034b99f71ae75e27b17ec210235ba410",
58+
"OG_0000012.fa.gz:md5,d03779dc8e61d42b7945d98c3263ef79",
59+
"HOG0000001.fa.gz:md5,4f2f37d12e4ff633a9b94e33a88e455a",
60+
"HOG0000002.fa.gz:md5,adfcb601ad79f42045f9af52265da97a",
61+
"HOG0000003.fa.gz:md5,1c0dd6e5d568daa80ffaf2181285bb11",
62+
"HOG0000004.fa.gz:md5,398d13abab8188b12b2974f435ada83b",
63+
"HOG0000005.fa.gz:md5,d84212a81ba4c7617b3fcc5a6fe19df3",
64+
"HOG0000006.fa.gz:md5,e16e7a970c10b0da63739fee1ce9fd13",
65+
"HOG0000007.fa.gz:md5,44be5719ddf0eead5eecc1efcb2020bb",
66+
"HOG0000008.fa.gz:md5,2fe75a29eeb184440dae58b0e293fc06",
67+
"HOG0000009.fa.gz:md5,f74a157bc1af82adb3a9b160d6de137a",
68+
"HOG0000010.fa.gz:md5,cd22e8c78937ba7ba1ef9224fe04732d",
69+
"HOG0000011.fa.gz:md5,034b99f71ae75e27b17ec210235ba410",
70+
"HOG0000012.fa.gz:md5,d03779dc8e61d42b7945d98c3263ef79",
7171
"phylostratigraphy.html:md5,060aafe142edbe56cd004090d695177d",
7272
"species_tree_checked.nwk:md5,4c82a2f2ffa72a595aaf2fd3deddeff7"
7373
],
7474
[
7575
{
7676
"name": "FastOMA_HOGs.orthoxml",
77-
"md5": "ac011cd1d734cae01beee5bcb5cda143"
77+
"lineCount": 162
78+
},
79+
{
80+
"name": "OrthologousGroups.tsv",
81+
"lineCount": 28
82+
},
83+
{
84+
"name": "RootHOGs.tsv",
85+
"lineCount": 28
7886
},
7987
{
8088
"name": "AQUAE.fa.hogmap",
81-
"md5": "7a8c848990c9dce91d6c50d48ae1ddd1"
89+
"lineCount": 20
8290
},
8391
{
8492
"name": "CHLTR.fa.hogmap",
85-
"md5": "f81877dc801f04e105dbedabe16c5cc0"
93+
"lineCount": 18
8694
},
8795
{
8896
"name": "MYCGE.fa.hogmap",
89-
"md5": "8715ee4eff99f751ca1d3d90b770574c"
97+
"lineCount": 14
98+
},
99+
{
100+
"name": "orthologs.tsv.gz",
101+
"lineCount": 18
90102
}
91103
]
92104
],
93105
"meta": {
94106
"nf-test": "0.9.3",
95107
"nextflow": "24.10.5"
96108
},
97-
"timestamp": "2025-10-14T16:11:27.355334"
109+
"timestamp": "2025-10-23T11:28:44.855077"
98110
}
99111
}

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