update snapshot

Author: CaroAMN

docs/output.md

@@ -123,7 +123,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 <details markdown="1">
 <summary>Output files</summary>
 
-- `process/`
+- `process/sampleID`
   - `*.json/*.csv`: Converted mat file
   </details>
 

subworkflows/local/numorph_preprocessing/tests/.nftignore

@@ -16,6 +16,6 @@ numorphintensity/*/variables/*.mat
 numorphintensity/*/samples/*.png
 numorphstitch/*/variables/*.mat
 numorph3dunet/*
-mat2json/*/{NM_variables,alignment_table,path_table,adj_params,thresholds, stitch_tforms}.json
-mat2json/*/*.csv
+mat2json/*/*/{NM_variables,alignment_table,path_table,adj_params,thresholds, stitch_tforms}.json
+mat2json/*/*/*.csv
 numorphstitch/*/stitched/*.{tif,tiff}

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

@@ -298,39 +298,27 @@
                 "unzip/TEST1/ctip2_topro/16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0620.ome.tif"
             ],
             [
-                "NM_variables.json:md5,1b22c511f6604478093cd5a27336c22b",
-                "alignment_table.json:md5,9f977c8bd72256b66ffd33a05f23b58b",
-                "path_table.json:md5,d7c64a9916ba01ce5ef0a4048f785f52",
                 "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0",
-                "NM_variables.json:md5,1b22c511f6604478093cd5a27336c22b",
-                "adj_params.json:md5,3d32b557fa92a091b5a9c752708f1e1c",
-                "path_table.json:md5,d7c64a9916ba01ce5ef0a4048f785f52",
-                "thresholds.json:md5,8cbd665a0e392c2ea6d6d5f0ef27c579",
-                "adj_params.json:md5,3d32b557fa92a091b5a9c752708f1e1c",
-                "adjusted_z.csv:md5,f37cf931821fb1520cb1aa9ffd3abc66",
-                "alignment_table.json:md5,9f977c8bd72256b66ffd33a05f23b58b",
-                "path_table.json:md5,d7c64a9916ba01ce5ef0a4048f785f52",
                 "stitch_tforms.json:md5,b5cc9b439f94631bee62e3f8315dd9aa",
-                "thresholds.json:md5,8cbd665a0e392c2ea6d6d5f0ef27c579",
                 "z_disp_matrix.json:md5,575020a27eee808b03c615e0a80ca506",
                 "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0",
                 "TEST1_ctip2_full.tif:md5,fb17be9f66140c674dad1c0eba3b7a2e",
                 "TEST1_topro_full.tif:md5,5e6784fc7062215bc6538ccccc49a5f4",
-                "z_displacement_align.mat:md5,69e4ea5417d2e9929924d58ea3fee882",
+                "z_displacement_align.mat:md5,e5590c38ae7838b277c4d18a4c58e31d",
                 "ctip2_1_1_11.tif:md5,fccec39adaa86a092dd7fca25b480234",
                 "ctip2_1_2_11.tif:md5,f7eb54ccc7add77d02d5463ff7898356",
                 "ctip2_2_1_11.tif:md5,684a579cc8df0800a11d2ff892c3938d",
                 "ctip2_2_2_11.tif:md5,5f4305e1581ccd4651fd750669e3b69a",
-                "flatfield_1.png:md5,29363dd62e89891004ca77ced21fcae7",
-                "flatfield_2.png:md5,61303ba0bd931945e3f394279865cd6b",
-                "tile_adj_1.png:md5,774ac5422679c05f7e669fc9dfd31e3d",
-                "tile_adj_2.png:md5,b31104698fbdaf7b17ee869d92bcbc9f",
+                "flatfield_1.png:md5,c6116cc26f181bcfb2dcccd5730de7f1",
+                "flatfield_2.png:md5,6e7d8007254091df9ae9604f66683eb6",
+                "tile_adj_1.png:md5,fb2765b262a8d379fdfcf0b7c16bff2f",
+                "tile_adj_2.png:md5,45698fa6940d1882761cb48d2801c899",
                 "topro_1_1_11.tif:md5,733e3e7bc32916dfcbc73c9c77404d69",
                 "topro_1_2_11.tif:md5,4652de23e14b9b3546c462d18a70e542",
                 "topro_2_1_11.tif:md5,918562924baffc0b99976837ef4b5121",
                 "topro_2_2_11.tif:md5,9f6a1c2b631a11cd675e96fd6e29c1b4",
-                "y_adj_1.png:md5,e8a8a26d9b587d52df189404680f64f1",
-                "y_adj_2.png:md5,e59bf4365580fa6bde6c208a729db09c",
+                "y_adj_1.png:md5,9d40dc840f18d1c5fac7bfbcd1daea6e",
+                "y_adj_2.png:md5,99e774585d742b2718f4c43c7f72a57d",
                 "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[02 x 02]_C00_xyz-Table Z0600.ome.tif:md5,5bceac0b61030e08808592c7bf3e8db0",
                 "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[02 x 02]_C00_xyz-Table Z0601.ome.tif:md5,da76c202e5baea80914bb2c0fb357aa3",
                 "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[02 x 02]_C00_xyz-Table Z0602.ome.tif:md5,f940ea6590a93301006d990bb1149c49",
@@ -505,6 +493,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-24T14:35:56.589951685"
+        "timestamp": "2025-09-24T21:22:26.778495001"
     }
 }

tests/.nftignore

@@ -17,6 +17,6 @@ numorphintensity/*/variables/*.mat
 numorphintensity/*/samples/*/*.png
 numorphstitch/*/variables/*.mat
 numorph3dunet/*/*
-mat2json/*/{NM_variables,alignment_table,path_table,adj_params,thresholds,stitch_tforms}.json
-mat2json/*/*.csv
+mat2json/*/*/{NM_variables,alignment_table,path_table,adj_params,thresholds,stitch_tforms}.json
+mat2json/*/*/*.csv
 numorphstitch/*/stitched/*.{tif,tiff}

tests/default.nf.test.snap

@@ -83,7 +83,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-24T14:01:25.473856988"
+        "timestamp": "2025-09-24T20:43:39.152536272"
     },
     "default test gpu": {
         "content": [
@@ -394,20 +394,7 @@
                 "unzip/TEST1/ctip2_topro/16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0620.ome.tif"
             ],
             [
-                "NM_variables.json:md5,08abd19caba2c66f820428fbd668c42c",
-                "alignment_table.json:md5,73a450711e7640133e6608fc4c85d56e",
-                "path_table.json:md5,e9d896f1d5c3cf049f7e27680a1dc38d",
                 "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0",
-                "NM_variables.json:md5,08abd19caba2c66f820428fbd668c42c",
-                "adj_params.json:md5,b2bd3cd15764f50af3f21e60ada4719e",
-                "path_table.json:md5,e9d896f1d5c3cf049f7e27680a1dc38d",
-                "thresholds.json:md5,5fac3c16f10a595297d1a8893a54424f",
-                "adj_params.json:md5,b2bd3cd15764f50af3f21e60ada4719e",
-                "adjusted_z.csv:md5,fb735d0a4d453fbd9356cd557488de16",
-                "alignment_table.json:md5,73a450711e7640133e6608fc4c85d56e",
-                "path_table.json:md5,e9d896f1d5c3cf049f7e27680a1dc38d",
-                "stitch_tforms.json:md5,b5cc9b439f94631bee62e3f8315dd9aa",
-                "thresholds.json:md5,5fac3c16f10a595297d1a8893a54424f",
                 "z_disp_matrix.json:md5,575020a27eee808b03c615e0a80ca506",
                 "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0",
                 "TEST1_ctip2_full.tif:md5,fb17be9f66140c674dad1c0eba3b7a2e",
@@ -594,6 +581,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.6"
         },
-        "timestamp": "2025-09-24T13:49:57.832786844"
+        "timestamp": "2025-09-24T17:34:33.965082839"
     }
 }