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Merge pull request #198 from nf-core/test-ci
Play around with CI
2 parents 57ffa05 + aabe87b commit 22f6c84

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10 files changed

+50
-46
lines changed

10 files changed

+50
-46
lines changed

‎modules/local/adata/entropy/tests/main.nf.test.snap

Lines changed: 6 additions & 6 deletions
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@@ -58,11 +58,11 @@
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{
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"id": "test"
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},
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"test_entropy.h5ad:md5,8adb6e8c8b0d363bc82b2e9a2d865c92"
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"test_entropy.h5ad:md5,fcb737603f514f4417d09c0a66b13e80"
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]
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],
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"1": [
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"test_entropy.pkl:md5,30379b39824af1d6e3a1a8765c50c761"
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"test_entropy.pkl:md5,a9fff140a3651204de06e77c3691eedd"
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],
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"2": [
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@@ -78,14 +78,14 @@
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{
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"id": "test"
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},
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"test_entropy.h5ad:md5,8adb6e8c8b0d363bc82b2e9a2d865c92"
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"test_entropy.h5ad:md5,fcb737603f514f4417d09c0a66b13e80"
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]
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],
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"multiqc_files": [
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],
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"obs": [
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"test_entropy.pkl:md5,30379b39824af1d6e3a1a8765c50c761"
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"test_entropy.pkl:md5,a9fff140a3651204de06e77c3691eedd"
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],
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"plots": [
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@@ -97,8 +97,8 @@
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-22T15:55:37.206313117"
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"timestamp": "2025-08-01T13:31:01.089437435"
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}
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}

‎modules/local/scanpy/leiden/tests/main.nf.test.snap

Lines changed: 6 additions & 6 deletions
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@@ -58,11 +58,11 @@
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{
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"id": "test"
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},
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"test_leiden.h5ad:md5,6b5cc4904f070c25dc10cc05ba2b1dbd"
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"test_leiden.h5ad:md5,e9c58f2cb8e7d6085461abc8353ed704"
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]
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],
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"1": [
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"test_leiden.pkl:md5,194f804c4eb94643da2bc22e1f7b821d"
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"test_leiden.pkl:md5,5af626f8508811356c83d60fd7c6e13a"
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],
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"2": [
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@@ -78,14 +78,14 @@
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{
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"id": "test"
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},
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"test_leiden.h5ad:md5,6b5cc4904f070c25dc10cc05ba2b1dbd"
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"test_leiden.h5ad:md5,e9c58f2cb8e7d6085461abc8353ed704"
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]
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],
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"multiqc_files": [
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],
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"obs": [
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"test_leiden.pkl:md5,194f804c4eb94643da2bc22e1f7b821d"
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"test_leiden.pkl:md5,5af626f8508811356c83d60fd7c6e13a"
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],
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"plots": [
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@@ -97,8 +97,8 @@
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-22T16:15:02.284151387"
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"timestamp": "2025-08-01T13:25:57.728739105"
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}
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}

‎modules/local/scanpy/neighbors/tests/main.nf.test.snap

Lines changed: 4 additions & 4 deletions
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@@ -40,7 +40,7 @@
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{
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"id": "test"
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},
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"test_neighbors.h5ad:md5,810e753759c7162ddb465ef3130d5d7a"
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"test_neighbors.h5ad:md5,8c37445ef7f23300a624b7985b94f959"
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]
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],
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"1": [
@@ -51,7 +51,7 @@
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{
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"id": "test"
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},
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"test_neighbors.h5ad:md5,810e753759c7162ddb465ef3130d5d7a"
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"test_neighbors.h5ad:md5,8c37445ef7f23300a624b7985b94f959"
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]
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],
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"versions": [
@@ -61,8 +61,8 @@
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-22T16:13:22.56806176"
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"timestamp": "2025-08-01T13:24:52.214682752"
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}
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}

‎modules/local/scanpy/pca/templates/pca.py

Lines changed: 2 additions & 2 deletions
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@@ -22,9 +22,9 @@
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# Run PCA
2323
sc.pp.pca(adata, random_state=0, key_added=key_added)
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25-
# Round to 10 decimal places
25+
# Round to 8 decimal places
2626
# This ensures hashes are stable
27-
adata.obsm[key_added] = np.round(adata.obsm[key_added], 10)
27+
adata.obsm[key_added] = np.round(adata.obsm[key_added], 8)
2828

2929
adata.write_h5ad(f"{prefix}.h5ad")
3030
df = pd.DataFrame(adata.obsm[key_added], index=adata.obs_names)

‎modules/local/scanpy/pca/tests/main.nf.test.snap

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@@ -46,11 +46,11 @@
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{
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"id": "test"
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},
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"test_pca.h5ad:md5,fc938377eb3d58bad59c42bab2d534b0"
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"test_pca.h5ad:md5,c21d37274dfe8f13c39fa3d91e415c9f"
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]
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],
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"1": [
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"X_test_pca.pkl:md5,31bb6b6ea07d25e1b3262349d5803106"
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"X_test_pca.pkl:md5,ee20fdc88c09d6aadf364af36631af81"
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],
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"2": [
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"versions.yml:md5,2773b6a3cada54f9812b357f83c33107"
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{
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"id": "test"
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},
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"test_pca.h5ad:md5,fc938377eb3d58bad59c42bab2d534b0"
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"test_pca.h5ad:md5,c21d37274dfe8f13c39fa3d91e415c9f"
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]
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],
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"obsm": [
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"X_test_pca.pkl:md5,31bb6b6ea07d25e1b3262349d5803106"
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"X_test_pca.pkl:md5,ee20fdc88c09d6aadf364af36631af81"
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],
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"versions": [
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"versions.yml:md5,2773b6a3cada54f9812b357f83c33107"
@@ -73,8 +73,8 @@
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-22T16:56:45.632782476"
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"timestamp": "2025-08-01T12:42:37.601905627"
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}
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}

‎modules/local/scanpy/umap/tests/main.nf.test.snap

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@@ -46,11 +46,11 @@
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{
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"id": "test"
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},
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"test.h5ad:md5,4a3eeb7c2d177bdd8fba5d68ce0a4542"
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"test.h5ad:md5,be511704be2e35160002c7c98a463bfc"
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]
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],
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"1": [
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"X_test.pkl:md5,05e0e45a8274a59496f188b0bba91208"
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"X_test.pkl:md5,398ed8a506a65f8bfa9e313a41c9d9ee"
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],
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"2": [
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"versions.yml:md5,8dd6b67d52121ffea06f0546bd248df7"
@@ -60,11 +60,11 @@
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{
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"id": "test"
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},
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"test.h5ad:md5,4a3eeb7c2d177bdd8fba5d68ce0a4542"
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"test.h5ad:md5,be511704be2e35160002c7c98a463bfc"
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]
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],
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"obsm": [
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"X_test.pkl:md5,05e0e45a8274a59496f188b0bba91208"
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"X_test.pkl:md5,398ed8a506a65f8bfa9e313a41c9d9ee"
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],
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"versions": [
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"versions.yml:md5,8dd6b67d52121ffea06f0546bd248df7"
@@ -73,8 +73,8 @@
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.3"
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-22T17:37:53.36398184"
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"timestamp": "2025-08-01T13:26:56.274070245"
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}
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}

‎modules/local/scimilarity/pseudobulk/tests/main.nf.test.snap

Lines changed: 5 additions & 5 deletions
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@@ -40,7 +40,7 @@
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{
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"id": "test"
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},
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"test_pseudobulk.h5ad:md5,ac245076ba4ee8dca4e0f0852d5c488e"
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"test_pseudobulk.h5ad:md5,34302d3c5058f4c987f1539d7d13359f"
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]
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],
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"1": [
@@ -51,7 +51,7 @@
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{
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"id": "test"
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},
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"test_pseudobulk.h5ad:md5,ac245076ba4ee8dca4e0f0852d5c488e"
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"test_pseudobulk.h5ad:md5,34302d3c5058f4c987f1539d7d13359f"
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]
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],
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"versions": [
@@ -60,10 +60,10 @@
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}
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],
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"meta": {
63-
"nf-test": "0.9.0",
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"nextflow": "25.04.2"
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-06-04T20:52:11.306872854"
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"timestamp": "2025-08-01T13:33:25.899199594"
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},
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"Should run without failures - stub": {
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"content": [

‎modules/local/scvitools/scanvi/tests/main.nf.test

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -77,10 +77,12 @@ nextflow_process {
7777
{ assert process.success },
7878
{ assert snapshot(
7979
// Hashes are not stable due to floating point inaccuracies
80-
file(process.out.h5ad.get(0).get(1)).size(),
81-
file(process.out.model.get(0).get(1)).size(),
82-
file(process.out.obsm.get(0)).size(),
83-
file(process.out.obs.get(0)).size(),
80+
file(process.out.h5ad[0][1]).size(),
81+
file(process.out.h5ad[0][1]).name,
82+
file(process.out.model[0][1]).size(),
83+
file(process.out.model[0][1]).name,
84+
file(process.out.obsm[0]).size(),
85+
file(process.out.obsm[0]).name,
8486
process.out.versions
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).match()
8688
},

‎modules/local/scvitools/scanvi/tests/main.nf.test.snap

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@@ -63,17 +63,19 @@
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"Should run without failures": {
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"content": [
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28863050,
66-
1375767,
66+
"test_scanvi.h5ad",
67+
1378327,
68+
"model.pt",
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6118418,
68-
1568819,
70+
"X_test_scanvi.pkl",
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[
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"versions.yml:md5,dcc5dcaf0ed31ba1d9695b817bd70d2d"
7173
]
7274
],
7375
"meta": {
7476
"nf-test": "0.9.2",
75-
"nextflow": "25.04.2"
77+
"nextflow": "25.04.6"
7678
},
77-
"timestamp": "2025-06-05T21:56:49.710035839"
79+
"timestamp": "2025-08-01T14:03:02.812639616"
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}
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}

‎subworkflows/local/quality_control/tests/main.nf.test.snap

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"batch_col": "sample",
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"counts_layer": "X"
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},
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"test.h5ad:md5,c22d5aca6a360de7dd852cdf2d6ac1be"
144+
"test.h5ad:md5,7cce8ecbdfcecc289ba13e0abf312269"
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]
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],
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"1": [
@@ -170,7 +170,7 @@
170170
"batch_col": "sample",
171171
"counts_layer": "X"
172172
},
173-
"test.h5ad:md5,c22d5aca6a360de7dd852cdf2d6ac1be"
173+
"test.h5ad:md5,7cce8ecbdfcecc289ba13e0abf312269"
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]
175175
],
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"multiqc_files": [
@@ -198,6 +198,6 @@
198198
"nf-test": "0.9.2",
199199
"nextflow": "25.04.6"
200200
},
201-
"timestamp": "2025-07-13T22:27:26.85479338"
201+
"timestamp": "2025-08-01T15:14:45.836429467"
202202
}
203203
}

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