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Merge pull request #256 from nf-core/singler-fix
Fix SingleR obs naming
2 parents 16160a5 + 712b488 commit aa2eeb9

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7 files changed

+78
-78
lines changed

7 files changed

+78
-78
lines changed

‎modules/local/celltypes/singler/templates/singleR.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -102,7 +102,7 @@ for (ref_idx in seq_along(references)) {
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)
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colnames(predictions) <- paste0(
105-
colnames(predictions), "_", prefix, "_", ref_name
105+
colnames(predictions), "_", ref_name
106106
)
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prediction_results[[ref]] <- predictions
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}

‎modules/local/celltypes/singler/tests/main.nf.test.snap‎

Lines changed: 22 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,7 @@
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{
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"id": "test"
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},
9-
"test_singler_predictions.csv:md5,1c31f07b4bff6980036f444039468fa5"
9+
"test_singler_predictions.csv:md5,b696e09b649235ac083de0d51a5f05fc"
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]
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],
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"test_singler_hpca_distribution.pdf",
@@ -15,11 +15,11 @@
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"versions.yml:md5,448f2705ce813b3f6e93bb74b092a60c"
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]
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],
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"timestamp": "2026-03-10T08:15:16.297363043",
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"meta": {
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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": "2025-08-02T10:33:18.632445193"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"Should run after celldex reference is fetched": {
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"content": [
@@ -28,7 +28,7 @@
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{
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"id": "test"
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},
31-
"test_singler_predictions.csv:md5,d90a4649a5d44b49f08568e58388f958"
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"test_singler_predictions.csv:md5,2b189f92b19bdd77f7fa202573a74b35"
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]
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],
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"test_singler_test_distribution.pdf",
@@ -37,11 +37,11 @@
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"versions.yml:md5,448f2705ce813b3f6e93bb74b092a60c"
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]
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],
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"timestamp": "2026-03-10T08:04:11.282862159",
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"meta": {
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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": "2025-08-02T10:21:19.878724413"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"Should run with a single reference": {
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"content": [
@@ -50,7 +50,7 @@
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{
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"id": "test"
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},
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"test_singler_predictions.csv:md5,1c31f07b4bff6980036f444039468fa5"
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"test_singler_predictions.csv:md5,b696e09b649235ac083de0d51a5f05fc"
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]
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],
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"test_singler_hpca_distribution.pdf",
@@ -59,11 +59,11 @@
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"versions.yml:md5,448f2705ce813b3f6e93bb74b092a60c"
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]
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],
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"timestamp": "2026-03-10T08:09:37.481752479",
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"meta": {
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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": "2025-08-02T10:27:18.432918231"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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},
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"Should run with a single reference - stub": {
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"content": [
@@ -124,11 +124,11 @@
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]
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}
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],
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"timestamp": "2025-08-02T11:42:02.21047184",
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"meta": {
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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": "2025-08-02T11:42:02.21047184"
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}
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},
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"Should run with two references": {
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"content": [
@@ -137,17 +137,17 @@
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{
138138
"id": "test"
139139
},
140-
"test_singler_predictions.csv:md5,67d0aa7d4534ec4d87ea7b28557e0441"
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"test_singler_predictions.csv:md5,11a52bcaca3f7e8ad88a9fe7d26b49c5"
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]
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],
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[
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"versions.yml:md5,448f2705ce813b3f6e93bb74b092a60c"
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]
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],
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"timestamp": "2026-03-10T08:21:48.883699278",
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"meta": {
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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": "2025-08-02T11:14:03.77950593"
149+
"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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}
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}

‎modules/local/hugounifier/apply/tests/main.nf.test.snap‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -26,11 +26,11 @@
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]
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}
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],
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"timestamp": "2026-01-10T23:17:20.422385507",
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
32-
},
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"timestamp": "2026-01-10T23:17:20.422385507"
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}
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},
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"Should run without failures": {
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"content": [
@@ -40,7 +40,7 @@
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{
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"id": "test"
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},
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"test_hugounifier.h5ad:md5,6a2e97a4b371b8774d6b8c22634eaa4b"
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"test_hugounifier.h5ad:md5,c7cdbd7262128dcbd7b90f845188e34f"
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]
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],
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"1": [
@@ -51,18 +51,18 @@
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{
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"id": "test"
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},
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"test_hugounifier.h5ad:md5,6a2e97a4b371b8774d6b8c22634eaa4b"
54+
"test_hugounifier.h5ad:md5,c7cdbd7262128dcbd7b90f845188e34f"
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]
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],
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"versions": [
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"versions.yml:md5,ecf9df8f7cb2a1ab5594ad9543ee32d7"
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]
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}
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],
62+
"timestamp": "2026-03-10T07:58:54.198227455",
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"meta": {
63-
"nf-test": "0.9.2",
64+
"nf-test": "0.9.4",
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"nextflow": "25.10.2"
65-
},
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"timestamp": "2026-02-15T18:59:48.493913413"
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}
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}
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}

‎modules/local/hugounifier/get/tests/main.nf.test.snap‎

Lines changed: 9 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -32,11 +32,11 @@
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]
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}
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],
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"timestamp": "2026-01-10T23:15:16.094519101",
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
38-
},
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"timestamp": "2026-01-10T23:15:16.094519101"
39+
}
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},
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"Should run without failures": {
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"content": [
@@ -47,8 +47,8 @@
4747
"id": "test"
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},
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[
50-
"sample1.csv:md5,1bde85720bbe0133cdcbe96df2fec192",
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"sample2.csv:md5,437d54f7d5db0eacb386873778a4eef1"
50+
"sample1.csv:md5,912f7444a187b1f8094c1f85b5282945",
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"sample2.csv:md5,bba30f28971437148138af65bd42aee0"
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]
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]
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],
@@ -61,8 +61,8 @@
6161
"id": "test"
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},
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[
64-
"sample1.csv:md5,1bde85720bbe0133cdcbe96df2fec192",
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"sample2.csv:md5,437d54f7d5db0eacb386873778a4eef1"
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"sample1.csv:md5,912f7444a187b1f8094c1f85b5282945",
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"sample2.csv:md5,bba30f28971437148138af65bd42aee0"
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]
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]
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],
@@ -71,10 +71,10 @@
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]
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}
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],
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"timestamp": "2026-03-10T07:56:17.593716871",
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"meta": {
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"nf-test": "0.9.2",
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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},
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"timestamp": "2026-02-15T17:21:28.944597088"
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}
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}
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}

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

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -28,11 +28,11 @@
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]
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}
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],
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"timestamp": "2025-07-13T13:35:35.117857167",
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"meta": {
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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": "2025-07-13T13:35:35.117857167"
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}
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},
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"Should run without failures": {
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"content": [
@@ -42,7 +42,7 @@
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{
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"id": "test"
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},
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"test_singler_predictions.csv:md5,a5912d3fb9dcba9f386286a332849ad4"
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"test_singler_predictions.csv:md5,dae3881eb387e231fccb6c4302d93077"
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]
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],
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"1": [
@@ -54,7 +54,7 @@
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{
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"id": "test"
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},
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"test_singler_predictions.csv:md5,a5912d3fb9dcba9f386286a332849ad4"
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"test_singler_predictions.csv:md5,dae3881eb387e231fccb6c4302d93077"
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]
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],
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"versions": [
@@ -63,10 +63,10 @@
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]
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}
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],
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"timestamp": "2026-03-10T09:08:21.0966997",
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"meta": {
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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": "2025-07-13T13:35:16.693586877"
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"nf-test": "0.9.4",
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"nextflow": "25.10.2"
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}
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}
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}

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

Lines changed: 15 additions & 15 deletions
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@@ -48,11 +48,11 @@
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]
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}
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],
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"timestamp": "2026-01-18T17:39:58.741250963",
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
54-
},
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"timestamp": "2026-01-18T17:39:58.741250963"
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}
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},
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"Should run without failures - symbol_col index, unify_gene_symbols false": {
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"content": [
@@ -101,11 +101,11 @@
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]
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}
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],
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"timestamp": "2026-01-18T21:22:29.899026309",
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"meta": {
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"nf-test": "0.9.2",
106107
"nextflow": "25.10.2"
107-
},
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"timestamp": "2026-01-18T21:22:29.899026309"
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}
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},
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"Should run without failures - symbol_col index, unify_gene_symbols true": {
111111
"content": [
@@ -121,7 +121,7 @@
121121
"unknown_label": "unknown",
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"counts_layer": "X"
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},
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"test_unified.h5ad:md5,720e333a51809a0ee9c03a9d1450d2ad"
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"test_unified.h5ad:md5,a9ac476adb2844de8640bf5fcaa0e0b9"
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]
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],
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"1": [
@@ -145,7 +145,7 @@
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"unknown_label": "unknown",
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"counts_layer": "X"
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},
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"test_unified.h5ad:md5,720e333a51809a0ee9c03a9d1450d2ad"
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"test_unified.h5ad:md5,a9ac476adb2844de8640bf5fcaa0e0b9"
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]
150150
],
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"multiqc_files": [
@@ -160,11 +160,11 @@
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]
161161
}
162162
],
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"timestamp": "2026-03-10T09:06:13.565614981",
163164
"meta": {
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"nf-test": "0.9.2",
165+
"nf-test": "0.9.4",
165166
"nextflow": "25.10.2"
166-
},
167-
"timestamp": "2026-02-15T18:59:00.665039292"
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}
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},
169169
"Should run without failures - symbol_col index, unify_gene_symbols false - stub": {
170170
"content": [
@@ -213,11 +213,11 @@
213213
]
214214
}
215215
],
216+
"timestamp": "2026-01-18T17:39:11.758025979",
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"meta": {
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"nf-test": "0.9.2",
218219
"nextflow": "25.04.6"
219-
},
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"timestamp": "2026-01-18T17:39:11.758025979"
220+
}
221221
},
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"Should run without failures - symbol_col index, unify_gene_symbols true - stub": {
223223
"content": [
@@ -274,11 +274,11 @@
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]
275275
}
276276
],
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"timestamp": "2026-01-18T17:41:17.198406767",
277278
"meta": {
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"nf-test": "0.9.2",
279280
"nextflow": "25.04.6"
280-
},
281-
"timestamp": "2026-01-18T17:41:17.198406767"
281+
}
282282
},
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"Should run without failures - symbol_col none, unify_gene_symbols false": {
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"content": [
@@ -329,10 +329,10 @@
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]
330330
}
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],
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"timestamp": "2026-01-18T21:23:44.819165812",
332333
"meta": {
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"nf-test": "0.9.2",
334335
"nextflow": "25.10.2"
335-
},
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"timestamp": "2026-01-18T21:23:44.819165812"
336+
}
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}
338338
}

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