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‎tests/default.nf.test‎

Lines changed: 17 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
11
nextflow_pipeline {
22

3-
name "Test Workflow METAPEP main.nf - test_mhcnuggets_2"
3+
name "Test Workflow METAPEP main.nf - test"
44
script "main.nf"
5-
profile "test_mhcnuggets_2"
5+
tag "test"
66
tag "pipeline"
77

8-
test("test mhcnuggets hla type 2 prediction") {
8+
test("test assembly and bin input") {
99

1010
when {
1111
params {
@@ -28,18 +28,21 @@ nextflow_pipeline {
2828
path("$outputDir/db_tables/microbiomes_entities.tsv"),
2929
path("$outputDir/db_tables/microbiomes.tsv"),
3030
path("$outputDir/db_tables/proteins_peptides.tsv"),
31+
path("$outputDir/db_tables/peptides.tsv.gz"),
32+
path("$outputDir/db_tables/proteins.tsv.gz"),
33+
path("$outputDir/db_tables/predictions.tsv.gz"),
3134
path("$outputDir/db_tables/stats.tsv")).match("db_tables") },
32-
{ assert snapshot(path("$outputDir/db_tables/peptides.tsv.gz").linesGzip.size()).match("peptides.tsv.gz")},
33-
{ assert snapshot(path("$outputDir/db_tables/proteins.tsv.gz").linesGzip.size()).match("proteins.tsv.gz")},
34-
{ assert snapshot(path("$outputDir/db_tables/predictions.tsv.gz").linesGzip.size()).match("predictions.tsv.gz")},
35-
{ assert new File("$outputDir/figures/entity_binding_ratios.DPB1_01_01.pdf").exists() },
36-
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.DPB1_01_01.pdf").exists() },
37-
{ assert new File("$outputDir/figures/prediction_score_distribution.DPB1_01_01.pdf").exists() },
38-
{ assert new File("$outputDir/figures/entity_binding_ratios.DQB1_02_02.pdf").exists() },
39-
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.DQB1_02_02.pdf").exists() },
40-
{ assert new File("$outputDir/figures/prediction_score_distribution.DQB1_02_02.pdf").exists() },
41-
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log")).match("logs") },
42-
{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
35+
{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
36+
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
37+
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
38+
{ assert new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
39+
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
40+
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
41+
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
42+
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },
43+
{ assert new File("$outputDir/prodigal/proteins.pred_0.bin.1.tsv.gz").exists() },
44+
{ assert new File("$outputDir/prodigal/proteins.pred_0.bin.2.tsv.gz").exists() },
45+
{ assert new File("$outputDir/prodigal/proteins.pred_1.tsv.gz").exists() }
4346
)
4447
}
4548

‎tests/default.nf.test.snap‎

Lines changed: 17 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -1,62 +1,36 @@
11
{
22
"db_tables": {
33
"content": [
4-
"alleles.tsv:md5,ab0e4dbbb55b8154d37256018c19d67c",
5-
"conditions_alleles.tsv:md5,769c299e94c7df654a5a14da2771c95d",
4+
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
5+
"conditions_alleles.tsv:md5,e865774e32935a69306461ff47428aa8",
66
"conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c",
7-
"entities_proteins.tsv:md5,2ba821a04755841dc6f116965f853f40",
8-
"entities.tsv:md5,61f364c97c883f45663ae27d115b229f",
9-
"microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19",
10-
"microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7",
11-
"microbiomes_entities.tsv:md5,6cef150e7f5fc2f3320d9a93da00f5de",
12-
"microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128",
13-
"proteins_peptides.tsv:md5,c2a16b2d30c9cf5ea52207dd799b4603",
14-
"stats.tsv:md5,8da7e6e2d9802fe424f09eeae7bcf98e"
7+
"entities_proteins.tsv:md5,fd4cbfeca8e8f176c9e2f7aff39921bf",
8+
"entities.tsv:md5,beb0a0fca43b5511cdabaf24bcc9113a",
9+
"microbiomes_entities.no_weights.tsv:md5,4d45837586c7c6dc4a19b41735215b01",
10+
"microbiomes_entities.nucl.tsv:md5,f5a3ff3cc1f8100f56238b9fab405e66",
11+
"microbiomes_entities.tsv:md5,ea5c9629387ee19ccc485af0157a922c",
12+
"microbiomes.tsv:md5,20f141ba0c97325e9d99a9c0765f9a37",
13+
"proteins_peptides.tsv:md5,e4d6b0199769075ff20c8eeca1485852",
14+
"peptides.tsv.gz:md5,66f6ceef1d5212d061b46c90703282d9",
15+
"proteins.tsv.gz:md5,3b397fc51074066efe2d31a5aff2abe3",
16+
"predictions.tsv.gz:md5,a50679d98e43e09858bf5f29ed222cd2",
17+
"stats.tsv:md5,0e58a492488a23f273b8993262043f5a"
1518
],
1619
"meta": {
1720
"nf-test": "0.9.2",
1821
"nextflow": "25.04.7"
1922
},
20-
"timestamp": "2025-09-29T09:34:37.566693963"
21-
},
22-
"peptides.tsv.gz": {
23-
"content": [
24-
82371
25-
],
26-
"meta": {
27-
"nf-test": "0.9.2",
28-
"nextflow": "25.04.7"
29-
},
30-
"timestamp": "2025-09-29T09:34:37.609431796"
23+
"timestamp": "2025-09-25T18:55:33.654464671"
3124
},
3225
"logs": {
3326
"content": [
34-
"prediction_warnings.log:md5,d3ff6ac2a68d620e8f5023f4ab16a1b9"
35-
],
36-
"meta": {
37-
"nf-test": "0.9.2",
38-
"nextflow": "25.04.7"
39-
},
40-
"timestamp": "2025-09-25T17:46:51.663649238"
41-
},
42-
"proteins.tsv.gz": {
43-
"content": [
44-
89
45-
],
46-
"meta": {
47-
"nf-test": "0.9.2",
48-
"nextflow": "25.04.7"
49-
},
50-
"timestamp": "2025-09-29T09:34:37.622750291"
51-
},
52-
"predictions.tsv.gz": {
53-
"content": [
54-
164741
27+
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
28+
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55"
5529
],
5630
"meta": {
5731
"nf-test": "0.9.2",
5832
"nextflow": "25.04.7"
5933
},
60-
"timestamp": "2025-09-29T09:34:37.665612229"
34+
"timestamp": "2025-09-25T18:55:38.905894093"
6135
}
6236
}

‎tests/pipeline/test_all.nf.test‎

Lines changed: 57 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,57 @@
1+
nextflow_pipeline {
2+
3+
name "Test Workflow METAPEP main.nf - test_all"
4+
script "main.nf"
5+
tag "test_all"
6+
tag "pipeline"
7+
8+
test("test all input path including protein downloads") {
9+
10+
when {
11+
params {
12+
outdir = "$outputDir"
13+
}
14+
}
15+
16+
then {
17+
assertAll(
18+
{ assert workflow.success },
19+
{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
20+
{ assert new File("$outputDir/pipeline_info/nf_core_metapep_software_mqc_versions.yml").exists() },
21+
{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
22+
path("$outputDir/db_tables/conditions_alleles.tsv"),
23+
path("$outputDir/db_tables/conditions.tsv"),
24+
path("$outputDir/db_tables/entities_proteins.tsv"),
25+
path("$outputDir/db_tables/entities.tsv"),
26+
path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"),
27+
path("$outputDir/db_tables/microbiomes_entities.nucl.tsv"),
28+
path("$outputDir/db_tables/microbiomes_entities.tsv"),
29+
path("$outputDir/db_tables/microbiomes.tsv"),
30+
path("$outputDir/db_tables/proteins_peptides.tsv"),
31+
path("$outputDir/db_tables/stats.tsv")).match("db_tables") },
32+
{ assert snapshot(path("$outputDir/db_tables/peptides.tsv.gz").linesGzip.size()).match("peptides.tsv.gz")},
33+
{ assert snapshot(path("$outputDir/db_tables/proteins.tsv.gz").linesGzip.size()).match("proteins.tsv.gz")},
34+
{ assert snapshot(path("$outputDir/db_tables/predictions.tsv.gz").linesGzip.size()).match("predictions.tsv.gz")},
35+
{ assert snapshot(path("$outputDir/entrez_data/microbiomes_entities.entrez.tsv")).match("entrez_data") },
36+
{ assert new File("$outputDir/entrez_data/entities_proteins.entrez.tsv").exists() },
37+
{ assert new File("$outputDir/entrez_data/proteins.entrez.tsv.gz").exists() },
38+
{ assert new File("$outputDir/entrez_data/taxa_assemblies.tsv").exists() },
39+
{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
40+
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
41+
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
42+
{ assert new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
43+
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
44+
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
45+
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
46+
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log"),
47+
path("$outputDir/logs/download_proteins.log")).match("logs") },
48+
{ assert new File("$outputDir/prodigal/proteins.pred_1.bin.1.tsv.gz").exists() },
49+
{ assert new File("$outputDir/prodigal/proteins.pred_1.bin.2.tsv.gz").exists() },
50+
{ assert new File("$outputDir/prodigal/proteins.pred_2.tsv.gz").exists() }
51+
)
52+
53+
}
54+
55+
}
56+
57+
}

‎tests/pipeline/test_all.nf.test.snap‎

Lines changed: 74 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,74 @@
1+
{
2+
"entrez_data": {
3+
"content": [
4+
"microbiomes_entities.entrez.tsv:md5,77463a684452d34795b6eda52cfad072"
5+
],
6+
"meta": {
7+
"nf-test": "0.9.2",
8+
"nextflow": "25.04.7"
9+
},
10+
"timestamp": "2025-09-25T17:01:13.725175386"
11+
},
12+
"db_tables": {
13+
"content": [
14+
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
15+
"conditions_alleles.tsv:md5,0e992c19471bb56c9b6e6a6f71302742",
16+
"conditions.tsv:md5,87707cd0dee14b0ca4face090ba9dce9",
17+
"entities_proteins.tsv:md5,cab71a940c16a82fc30ec1648ce3ed12",
18+
"entities.tsv:md5,b7d3d019c258859c93bbc15095d304f1",
19+
"microbiomes_entities.no_weights.tsv:md5,19a44189e6977fc64b78198ad609507a",
20+
"microbiomes_entities.nucl.tsv:md5,aa0d4cc3546508c8e5b81bc9b4b16e39",
21+
"microbiomes_entities.tsv:md5,d2e975e7a324eb0595bd4af37376d144",
22+
"microbiomes.tsv:md5,70871c8b3023f5a8412c05f4a69dda2f",
23+
"proteins_peptides.tsv:md5,9fd528d928349164cc10e63da2c67fe8",
24+
"stats.tsv:md5,49e094222e02cd592cd1daff6dd9778f"
25+
],
26+
"meta": {
27+
"nf-test": "0.9.2",
28+
"nextflow": "25.04.7"
29+
},
30+
"timestamp": "2025-09-29T08:18:29.790035039"
31+
},
32+
"peptides.tsv.gz": {
33+
"content": [
34+
5932765
35+
],
36+
"meta": {
37+
"nf-test": "0.9.2",
38+
"nextflow": "25.04.7"
39+
},
40+
"timestamp": "2025-09-29T08:18:31.341839622"
41+
},
42+
"logs": {
43+
"content": [
44+
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
45+
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55",
46+
"download_proteins.log:md5,2df710939b3d7a2bbcb3c962817b8538"
47+
],
48+
"meta": {
49+
"nf-test": "0.9.2",
50+
"nextflow": "25.04.7"
51+
},
52+
"timestamp": "2025-09-26T11:05:02.756392866"
53+
},
54+
"proteins.tsv.gz": {
55+
"content": [
56+
6994
57+
],
58+
"meta": {
59+
"nf-test": "0.9.2",
60+
"nextflow": "25.04.7"
61+
},
62+
"timestamp": "2025-09-29T08:18:31.805072233"
63+
},
64+
"predictions.tsv.gz": {
65+
"content": [
66+
11783496
67+
],
68+
"meta": {
69+
"nf-test": "0.9.2",
70+
"nextflow": "25.04.7"
71+
},
72+
"timestamp": "2025-09-29T08:18:33.890885942"
73+
}
74+
}

‎tests/pipeline/test_assembly_only.nf.test‎

Lines changed: 49 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,49 @@
1+
nextflow_pipeline {
2+
3+
name "Test Workflow METAPEP main.nf - test_assembly_only"
4+
script "main.nf"
5+
profile "test_assembly_only"
6+
tag "pipeline"
7+
8+
test("test assembly input") {
9+
10+
when {
11+
params {
12+
outdir = "$outputDir"
13+
}
14+
}
15+
16+
then {
17+
assertAll(
18+
{ assert workflow.success },
19+
{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
20+
{ assert new File("$outputDir/pipeline_info/nf_core_metapep_software_mqc_versions.yml").exists() },
21+
{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
22+
path("$outputDir/db_tables/conditions_alleles.tsv"),
23+
path("$outputDir/db_tables/conditions.tsv"),
24+
path("$outputDir/db_tables/entities_proteins.tsv"),
25+
path("$outputDir/db_tables/entities.tsv"),
26+
path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"),
27+
path("$outputDir/db_tables/microbiomes_entities.nucl.tsv"),
28+
path("$outputDir/db_tables/microbiomes_entities.tsv"),
29+
path("$outputDir/db_tables/microbiomes.tsv"),
30+
path("$outputDir/db_tables/proteins_peptides.tsv"),
31+
path("$outputDir/db_tables/stats.tsv")).match("db_tables") },
32+
{ assert snapshot(path("$outputDir/db_tables/peptides.tsv.gz").linesGzip.size()).match("peptides.tsv.gz")},
33+
{ assert snapshot(path("$outputDir/db_tables/proteins.tsv.gz").linesGzip.size()).match("proteins.tsv.gz")},
34+
{ assert snapshot(path("$outputDir/db_tables/predictions.tsv.gz").linesGzip.size()).match("predictions.tsv.gz")},
35+
{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
36+
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
37+
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
38+
{ assert new File("$outputDir/figures/entity_binding_ratios.B_07_02.pdf").exists() },
39+
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.B_07_02.pdf").exists() },
40+
{ assert new File("$outputDir/figures/prediction_score_distribution.B_07_02.pdf").exists() },
41+
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
42+
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },
43+
{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
44+
)
45+
}
46+
47+
}
48+
49+
}

‎tests/pipeline/test_assembly_only.nf.test.snap‎

Lines changed: 63 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,63 @@
1+
{
2+
"db_tables": {
3+
"content": [
4+
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
5+
"conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f",
6+
"conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c",
7+
"entities_proteins.tsv:md5,2ba821a04755841dc6f116965f853f40",
8+
"entities.tsv:md5,61f364c97c883f45663ae27d115b229f",
9+
"microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19",
10+
"microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7",
11+
"microbiomes_entities.tsv:md5,6cef150e7f5fc2f3320d9a93da00f5de",
12+
"microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128",
13+
"proteins_peptides.tsv:md5,c2a16b2d30c9cf5ea52207dd799b4603",
14+
"stats.tsv:md5,e928505fe659aaac51846b57c7ecfc43"
15+
],
16+
"meta": {
17+
"nf-test": "0.9.2",
18+
"nextflow": "25.04.7"
19+
},
20+
"timestamp": "2025-09-29T08:19:48.377351802"
21+
},
22+
"peptides.tsv.gz": {
23+
"content": [
24+
82371
25+
],
26+
"meta": {
27+
"nf-test": "0.9.2",
28+
"nextflow": "25.04.7"
29+
},
30+
"timestamp": "2025-09-29T08:19:48.427421332"
31+
},
32+
"logs": {
33+
"content": [
34+
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
35+
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55"
36+
],
37+
"meta": {
38+
"nf-test": "0.9.2",
39+
"nextflow": "25.04.7"
40+
},
41+
"timestamp": "2025-09-25T16:52:08.223882859"
42+
},
43+
"proteins.tsv.gz": {
44+
"content": [
45+
89
46+
],
47+
"meta": {
48+
"nf-test": "0.9.2",
49+
"nextflow": "25.04.7"
50+
},
51+
"timestamp": "2025-09-29T08:19:48.441733117"
52+
},
53+
"predictions.tsv.gz": {
54+
"content": [
55+
164741
56+
],
57+
"meta": {
58+
"nf-test": "0.9.2",
59+
"nextflow": "25.04.7"
60+
},
61+
"timestamp": "2025-09-29T08:19:48.472733118"
62+
}
63+
}

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