From 37ef37fd42306b1bb2ed58d5637ead610c83c6a2 Mon Sep 17 00:00:00 2001 From: RobJY Date: Fri, 17 Jan 2025 12:41:43 -0500 Subject: [PATCH 1/2] testing what seems to be more correct test cases --- .../deepcell/mesmer/tests/main.nf.test | 2 +- tests/main.nf.test | 56 +++++++++---------- 2 files changed, 29 insertions(+), 29 deletions(-) diff --git a/modules/nf-core/deepcell/mesmer/tests/main.nf.test b/modules/nf-core/deepcell/mesmer/tests/main.nf.test index 248fa550..da226b6a 100644 --- a/modules/nf-core/deepcell/mesmer/tests/main.nf.test +++ b/modules/nf-core/deepcell/mesmer/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id: 'test_img' ], - file(params.modules_testdata_base_path + '/modules/data/imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) + file(params.modules_testdata_base_path + '/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true) ] input[1] = [ [:], diff --git a/tests/main.nf.test b/tests/main.nf.test index 23289808..7a64fcf5 100644 --- a/tests/main.nf.test +++ b/tests/main.nf.test @@ -171,14 +171,14 @@ nextflow_workflow { [2,1,'ELANE',[],[],[],[],[],[]], [3,1,'CD57',[],[],[],[],[],[]], [4,1,'CD45',[],[],[],[],[],[]], - [5,1,'DNA_7',[],[],[],[],[],[]], - [6,1,'ELANE7',[],[],[],[],[],[]], - [7,1,'CD577',[],[],[],[],[],[]], - [8,1,'CD457',[],[],[],[],[],[]], - [9,1,'DNA_8',[],[],[],[],[],[]], - [10,1,'ELANE8',[],[],[],[],[],[]], - [11,1,'CD578',[],[],[],[],[],[]], - [12,1,'CD458',[],[],[],[],[],[]], + [5,2,'DNA_7',[],[],[],[],[],[]], + [6,2,'ELANE7',[],[],[],[],[],[]], + [7,2,'CD577',[],[],[],[],[],[]], + [8,2,'CD457',[],[],[],[],[],[]], + [9,3,'DNA_8',[],[],[],[],[],[]], + [10,3,'ELANE8',[],[],[],[],[],[]], + [11,3,'CD578',[],[],[],[],[],[]], + [12,3,'CD458',[],[],[],[],[],[]], ], ) """ @@ -239,10 +239,10 @@ nextflow_workflow { [2,1,'ELANE',[],[],[],[],[],[]], [3,1,'CD57',[],[],[],[],[],[]], [4,1,'CD45',[],[],[],[],[],[]], - [5,1,'DNA_7',[],[],[],[],[],[]], - [6,1,'ELANE7',[],[],[],[],[],[]], - [7,1,'CD577',[],[],[],[],[],[]], - [8,1,'CD457',[],[],[],[],[],[]], + [5,2,'DNA_7',[],[],[],[],[],[]], + [6,2,'ELANE7',[],[],[],[],[],[]], + [7,2,'CD577',[],[],[],[],[],[]], + [8,2,'CD457',[],[],[],[],[],[]], ], ) """ @@ -306,10 +306,10 @@ nextflow_workflow { [2,1,'ELANE',[],[],[],[],[],[]], [3,1,'CD57',[],[],[],[],[],[]], [4,1,'CD45',[],[],[],[],[],[]], - [5,1,'DNA_7',[],[],[],[],[],[]], - [6,1,'ELANE7',[],[],[],[],[],[]], - [7,1,'CD577',[],[],[],[],[],[]], - [8,1,'CD457',[],[],[],[],[],[]], + [5,2,'DNA_7',[],[],[],[],[],[]], + [6,2,'ELANE7',[],[],[],[],[],[]], + [7,2,'CD577',[],[],[],[],[],[]], + [8,2,'CD457',[],[],[],[],[],[]], ], ) """ @@ -372,14 +372,14 @@ nextflow_workflow { [2,1,'ELANE',[],[],[],[],[],[]], [3,1,'CD57',[],[],[],[],[],[]], [4,1,'CD45',[],[],[],[],[],[]], - [5,1,'DNA_7',[],[],[],[],[],[]], - [6,1,'ELANE7',[],[],[],[],[],[]], - [7,1,'CD577',[],[],[],[],[],[]], - [8,1,'CD457',[],[],[],[],[],[]], - [9,1,'DNA_8',[],[],[],[],[],[]], - [10,1,'ELANE8',[],[],[],[],[],[]], - [11,1,'CD578',[],[],[],[],[],[]], - [12,1,'CD458',[],[],[],[],[],[]], + [5,2,'DNA_7',[],[],[],[],[],[]], + [6,2,'ELANE7',[],[],[],[],[],[]], + [7,2,'CD577',[],[],[],[],[],[]], + [8,2,'CD457',[],[],[],[],[],[]], + [9,3,'DNA_8',[],[],[],[],[],[]], + [10,3,'ELANE8',[],[],[],[],[],[]], + [11,3,'CD578',[],[],[],[],[],[]], + [12,3,'CD458',[],[],[],[],[],[]], ], ) """ @@ -447,10 +447,10 @@ nextflow_workflow { [2,1,'ELANE',[],[],[],[],[],[]], [3,1,'CD57',[],[],[],[],[],[]], [4,1,'CD45',[],[],[],[],[],[]], - [5,1,'DNA_7',[],[],[],[],[],[]], - [6,1,'ELANE7',[],[],[],[],[],[]], - [7,1,'CD577',[],[],[],[],[],[]], - [8,1,'CD457',[],[],[],[],[],[]], + [5,2,'DNA_7',[],[],[],[],[],[]], + [6,2,'ELANE7',[],[],[],[],[],[]], + [7,2,'CD577',[],[],[],[],[],[]], + [8,2,'CD457',[],[],[],[],[],[]], ], ) """ From fe2e7cfdad1224a13d7ed56efb9dfb17292aecc8 Mon Sep 17 00:00:00 2001 From: RobJY Date: Fri, 17 Jan 2025 15:33:37 -0500 Subject: [PATCH 2/2] different issue I wanted to test; will look into it after we resolve the multicycle issue; reverting for now --- modules/nf-core/deepcell/mesmer/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/deepcell/mesmer/tests/main.nf.test b/modules/nf-core/deepcell/mesmer/tests/main.nf.test index da226b6a..248fa550 100644 --- a/modules/nf-core/deepcell/mesmer/tests/main.nf.test +++ b/modules/nf-core/deepcell/mesmer/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id: 'test_img' ], - file(params.modules_testdata_base_path + '/imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true) + file(params.modules_testdata_base_path + '/modules/data/imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) ] input[1] = [ [:],