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nf-test assertions #128

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merged 5 commits into from
Aug 6, 2024
Merged

nf-test assertions #128

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57fd30a
nf-test assertions
tillenglert Jul 18, 2024
5ffeb38
Add nf-test snapshots
tillenglert Jul 18, 2024
76ce8da
updated snaps to new sorting strategy
tillenglert Aug 5, 2024
e431d5b
Merge branch 'dev' into nf-test_assertions_new
tillenglert Aug 6, 2024
707375c
remove bank lines from *.nf.test
tillenglert Aug 6, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ jobs:

- name: Run nf-test
run: |
nf-test test --tag ${{ matrix.profile }} --profile ${{ matrix.profile }},docker --junitxml=test.xml
nf-test test --tag ${{ matrix.profile }} --profile ${{ matrix.profile }},docker --junitxml=test.xml --verbose

- name: Output log on failure
if: failure()
Expand Down Expand Up @@ -112,7 +112,7 @@ jobs:
run: |
nextflow secrets set NCBI_EMAIL ${{ secrets.NCBI_EMAIL }}
nextflow secrets set NCBI_KEY ${{ secrets.NCBI_KEY }}
nf-test test --tag ${{ matrix.profile }} --profile ${{ matrix.profile }},docker --junitxml=test.xml
nf-test test --tag ${{ matrix.profile }} --profile ${{ matrix.profile }},docker --junitxml=test.xml --verbose

- name: Output log on failure
if: failure()
Expand Down
28 changes: 27 additions & 1 deletion tests/pipeline/test.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,33 @@ nextflow_pipeline {
}

then {
assert workflow.success
assertAll(
{ assert workflow.success },
{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
path("$outputDir/db_tables/entities_proteins.tsv"),
path("$outputDir/db_tables/entities.tsv"),
path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"),
path("$outputDir/db_tables/microbiomes_entities.nucl.tsv"),
path("$outputDir/db_tables/microbiomes_entities.tsv"),
path("$outputDir/db_tables/microbiomes.tsv"),
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.bin.1.tsv.gz").exists() },
{ assert new File("$outputDir/prodigal/proteins.pred_0.bin.2.tsv.gz").exists() },
{ assert new File("$outputDir/prodigal/proteins.pred_1.tsv.gz").exists() }
)
}

}
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36 changes: 36 additions & 0 deletions tests/pipeline/test.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
{
"db_tables": {
"content": [
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,e865774e32935a69306461ff47428aa8",
"conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c",
"entities_proteins.tsv:md5,fd4cbfeca8e8f176c9e2f7aff39921bf",
"entities.tsv:md5,beb0a0fca43b5511cdabaf24bcc9113a",
"microbiomes_entities.no_weights.tsv:md5,4d45837586c7c6dc4a19b41735215b01",
"microbiomes_entities.nucl.tsv:md5,f5a3ff3cc1f8100f56238b9fab405e66",
"microbiomes_entities.tsv:md5,ea5c9629387ee19ccc485af0157a922c",
"microbiomes.tsv:md5,20f141ba0c97325e9d99a9c0765f9a37",
"proteins_peptides.tsv:md5,e4d6b0199769075ff20c8eeca1485852",
"peptides.tsv.gz:md5,66f6ceef1d5212d061b46c90703282d9",
"proteins.tsv.gz:md5,3b397fc51074066efe2d31a5aff2abe3",
"predictions.tsv.gz:md5,a50679d98e43e09858bf5f29ed222cd2",
"stats.txt:md5,83204291158696ce5d19c4e976f38efe"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
},
"timestamp": "2024-08-02T07:24:38.491278622"
},
"logs": {
"content": [
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
}
}
34 changes: 33 additions & 1 deletion tests/pipeline/test_all.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,39 @@ nextflow_pipeline {
}

then {
assert workflow.success
assertAll(
{ assert workflow.success },
{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
path("$outputDir/db_tables/entities_proteins.tsv"),
path("$outputDir/db_tables/entities.tsv"),
path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"),
path("$outputDir/db_tables/microbiomes_entities.nucl.tsv"),
path("$outputDir/db_tables/microbiomes_entities.tsv"),
path("$outputDir/db_tables/microbiomes.tsv"),
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert snapshot(path("$outputDir/entrez_data/microbiomes_entities.entrez.tsv")).match("entrez_data") },
{ assert new File("$outputDir/entrez_data/entities_proteins.entrez.tsv").exists() },
{ assert new File("$outputDir/entrez_data/proteins.entrez.tsv.gz").exists() },
{ assert new File("$outputDir/entrez_data/taxa_assemblies.tsv").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log"),
path("$outputDir/logs/download_proteins.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_1.bin.1.tsv.gz").exists() },
{ assert new File("$outputDir/prodigal/proteins.pred_1.bin.2.tsv.gz").exists() },
{ assert new File("$outputDir/prodigal/proteins.pred_2.tsv.gz").exists() }
)

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}

}
Expand Down
47 changes: 47 additions & 0 deletions tests/pipeline/test_all.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
{
"entrez_data": {
"content": [
"microbiomes_entities.entrez.tsv:md5,77463a684452d34795b6eda52cfad072"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
},
"db_tables": {
"content": [
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,0e992c19471bb56c9b6e6a6f71302742",
"conditions.tsv:md5,87707cd0dee14b0ca4face090ba9dce9",
"entities_proteins.tsv:md5,57a704e833a65a1809c369452864e241",
"entities.tsv:md5,b7d3d019c258859c93bbc15095d304f1",
"microbiomes_entities.no_weights.tsv:md5,977da228f562b386b0f84fc718cc22e9",
"microbiomes_entities.nucl.tsv:md5,aa0d4cc3546508c8e5b81bc9b4b16e39",
"microbiomes_entities.tsv:md5,03309271d7a983c7b4a5c73418676bbc",
"microbiomes.tsv:md5,70871c8b3023f5a8412c05f4a69dda2f",
"proteins_peptides.tsv:md5,aff145bbff9f962891db2c2a540242c4",
"peptides.tsv.gz:md5,36aba6d50b1aad95859a547b06d04fc5",
"proteins.tsv.gz:md5,027823577635c591b58326410b039b32",
"predictions.tsv.gz:md5,d3b36995f3b4027d1a14e726a0acc6c2",
"stats.txt:md5,896155e0f043f30bd71c38c8ee7b466c"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
},
"timestamp": "2024-08-02T07:59:44.990798256"
},
"logs": {
"content": [
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55",
"download_proteins.log:md5,488e1962cf079d466188481d526495f2"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-17T15:58:41.467969153"
}
}
26 changes: 25 additions & 1 deletion tests/pipeline/test_assembly_only.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,31 @@ nextflow_pipeline {
}

then {
assert workflow.success
assertAll(
{ assert workflow.success },
{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
path("$outputDir/db_tables/entities_proteins.tsv"),
path("$outputDir/db_tables/entities.tsv"),
path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"),
path("$outputDir/db_tables/microbiomes_entities.nucl.tsv"),
path("$outputDir/db_tables/microbiomes_entities.tsv"),
path("$outputDir/db_tables/microbiomes.tsv"),
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() }
)
}

}
Expand Down
36 changes: 36 additions & 0 deletions tests/pipeline/test_assembly_only.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
{
"db_tables": {
"content": [
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f",
"conditions.tsv:md5,a6fe5daaf11a90b61c83c9934969c52c",
"entities_proteins.tsv:md5,2ba821a04755841dc6f116965f853f40",
"entities.tsv:md5,61f364c97c883f45663ae27d115b229f",
"microbiomes_entities.no_weights.tsv:md5,bd449dafeb86c374552f2e22a9780b19",
"microbiomes_entities.nucl.tsv:md5,3888070b634251c0ae3e9fd4857140d7",
"microbiomes_entities.tsv:md5,6cef150e7f5fc2f3320d9a93da00f5de",
"microbiomes.tsv:md5,3d597aec25752f7ca83436b31bfaa128",
"proteins_peptides.tsv:md5,c2a16b2d30c9cf5ea52207dd799b4603",
"peptides.tsv.gz:md5,dd0f94bea5079df8ef06895de255038b",
"proteins.tsv.gz:md5,104b786dfa89e183a46e29f1f37f17de",
"predictions.tsv.gz:md5,98eeb5672f338ad5e8de7e2047261037",
"stats.txt:md5,d138e30d814db5203a789b7eddd04732"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
},
"timestamp": "2024-08-01T12:28:55.298980309"
},
"logs": {
"content": [
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
}
}
26 changes: 25 additions & 1 deletion tests/pipeline/test_bins_only.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,31 @@ nextflow_pipeline {
}

then {
assert workflow.success
assertAll(
{ assert workflow.success },
{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
path("$outputDir/db_tables/entities_proteins.tsv"),
path("$outputDir/db_tables/entities.tsv"),
path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"),
path("$outputDir/db_tables/microbiomes_entities.nucl.tsv"),
path("$outputDir/db_tables/microbiomes_entities.tsv"),
path("$outputDir/db_tables/microbiomes.tsv"),
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.bin.1.tsv.gz").exists() }
)
}

}
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36 changes: 36 additions & 0 deletions tests/pipeline/test_bins_only.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
{
"db_tables": {
"content": [
"alleles.tsv:md5,77994270b1eab3e8363c90d8d09780fa",
"conditions_alleles.tsv:md5,9db7e0afc739b23c430877e336b0143f",
"conditions.tsv:md5,5b04349198a406fc16760c7e8808bb23",
"entities_proteins.tsv:md5,20e495ff06ccacb0f81dbd65e556fc83",
"entities.tsv:md5,7a472316b8e96e9b12d7ca3ff6a88d39",
"microbiomes_entities.no_weights.tsv:md5,bf3ff9d0390b49c6ecafd89c93909b67",
"microbiomes_entities.nucl.tsv:md5,84b6b907695caaddc959682504749832",
"microbiomes_entities.tsv:md5,2f40573eb52f3d823aad2f09a639eee2",
"microbiomes.tsv:md5,3f58c3029d21a59316861c28af4361d1",
"proteins_peptides.tsv:md5,50df6a9278679870190795d7b7968113",
"peptides.tsv.gz:md5,34497a1a57af3c3e48fceb762cf94f75",
"proteins.tsv.gz:md5,1ae4d6be0e8bc4beb3d225aed3379d1c",
"predictions.tsv.gz:md5,1dd8ab58446c326432beadb44a0b327a",
"stats.txt:md5,62d598a845aff61f2be843daa250f485"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.3"
},
"timestamp": "2024-08-01T13:39:59.996820893"
},
"logs": {
"content": [
"prediction_warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e",
"SUCCEEDED_unify_peptide_lengths.log:md5,c27fb56e478b975c57c910011935dd55"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-26T08:14:54+0000"
}
}
28 changes: 27 additions & 1 deletion tests/pipeline/test_coassembly.nf.test
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,33 @@ nextflow_pipeline {
}

then {
assert workflow.success
assertAll(
{ assert workflow.success },
{ assert new File("$outputDir/multiqc/multiqc_report.html").exists() },
{ assert new File("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").exists() },
{ assert snapshot(path("$outputDir/db_tables/alleles.tsv"),
path("$outputDir/db_tables/conditions_alleles.tsv"),
path("$outputDir/db_tables/conditions.tsv"),
path("$outputDir/db_tables/entities_proteins.tsv"),
path("$outputDir/db_tables/entities.tsv"),
path("$outputDir/db_tables/microbiomes_entities.no_weights.tsv"),
path("$outputDir/db_tables/microbiomes_entities.nucl.tsv"),
path("$outputDir/db_tables/microbiomes_entities.tsv"),
path("$outputDir/db_tables/microbiomes.tsv"),
path("$outputDir/db_tables/proteins_peptides.tsv"),
path("$outputDir/db_tables/peptides.tsv.gz"),
path("$outputDir/db_tables/proteins.tsv.gz"),
path("$outputDir/db_tables/predictions.tsv.gz"),
path("$outputDir/db_tables/stats.txt")).match("db_tables") },
{ assert new File("$outputDir/figures/entity_binding_ratios.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/entity_binding_ratios.with_points.A_01_01.pdf").exists() },
{ assert new File("$outputDir/figures/prediction_score_distribution.A_01_01.pdf").exists() },
{ assert snapshot(path("$outputDir/logs/prediction_warnings.log"),
path("$outputDir/logs/SUCCEEDED_unify_peptide_lengths.log")).match("logs") },
{ assert new File("$outputDir/prodigal/proteins.pred_0.tsv.gz").exists() },
{ assert new File("$outputDir/prodigal/proteins.pred_1.bin.1.tsv.gz").exists() },
{ assert new File("$outputDir/prodigal/proteins.pred_1.bin.2.tsv.gz").exists() }
)
}

}
Expand Down
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