diff --git a/subworkflows/sanger/tiled_segmentation/main.nf b/subworkflows/sanger/tiled_segmentation/main.nf index 975ee9b8c99..0f1f7538c42 100644 --- a/subworkflows/sanger/tiled_segmentation/main.nf +++ b/subworkflows/sanger/tiled_segmentation/main.nf @@ -13,14 +13,13 @@ workflow TILED_SEGMENTATION { main: ch_versions = Channel.empty() - ch_images = Channel.of(images) - GENERATE_TILE_COORDS(ch_images) + GENERATE_TILE_COORDS(images) ch_versions = ch_versions.mix(GENERATE_TILE_COORDS.out.versions.first()) images_tiles = GENERATE_TILE_COORDS.out.tile_coords.splitCsv(header:true, sep:",").map{ meta, coords -> [meta, coords.X_MIN, coords.Y_MIN, coords.X_MAX, coords.Y_MAX] } - tiles_and_images = images_tiles.combine(ch_images, by:0) + tiles_and_images = images_tiles.combine(images, by:0) if (method == "CELLPOSE") { CELLPOSE(tiles_and_images.combine(channel.from(params.cell_diameters))) wkts = CELLPOSE.out.wkts.groupTuple(by:0) @@ -44,6 +43,6 @@ workflow TILED_SEGMENTATION { ch_versions = ch_versions.mix(MERGEOUTLINES.out.versions.first()) emit: - wkt = MERGEOUTLINES.out.multipoly_geojsons // channel: [ val(meta), [ geojson ] ] + geojson = MERGEOUTLINES.out.multipoly_geojsons // channel: [ val(meta), [ geojson ] ] versions = ch_versions // channel: [ versions.yml ] } \ No newline at end of file diff --git a/subworkflows/sanger/tiled_segmentation/tests/main.nf.test b/subworkflows/sanger/tiled_segmentation/tests/main.nf.test index e986f341373..71e58bc4c5e 100644 --- a/subworkflows/sanger/tiled_segmentation/tests/main.nf.test +++ b/subworkflows/sanger/tiled_segmentation/tests/main.nf.test @@ -17,10 +17,10 @@ nextflow_workflow { } workflow { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'imaging/segmentation/nuclear_image.tif', checkIfExists: true), - ] + ]) input[1] = 'CELLPOSE' """ } @@ -40,10 +40,10 @@ nextflow_workflow { when { workflow { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'imaging/segmentation/nuclear_image.tif', checkIfExists: true), - ] + ]) input[1] = 'STARDIST' """ } @@ -63,10 +63,10 @@ nextflow_workflow { when { workflow { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'imaging/segmentation/nuclear_image.tif', checkIfExists: true), - ] + ]) input[1] = 'INSTANSEG' """ } @@ -86,10 +86,10 @@ nextflow_workflow { when { workflow { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test'], // meta map file(params.modules_testdata_base_path + 'imaging/segmentation/nuclear_image.tif', checkIfExists: true), - ] + ]) input[1] = 'DEEPCELL' """ } diff --git a/subworkflows/sanger/tiled_segmentation/tests/main.nf.test.snap b/subworkflows/sanger/tiled_segmentation/tests/main.nf.test.snap index 6cc214da33e..7886911256e 100644 --- a/subworkflows/sanger/tiled_segmentation/tests/main.nf.test.snap +++ b/subworkflows/sanger/tiled_segmentation/tests/main.nf.test.snap @@ -15,18 +15,18 @@ "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", "versions.yml:md5,74ae9680e8565f16244a79acbe2ef1e4" ], - "versions": [ - "versions.yml:md5,1d6e2b331dc05b3496a477c7e8adbeee", - "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", - "versions.yml:md5,74ae9680e8565f16244a79acbe2ef1e4" - ], - "wkt": [ + "geojson": [ [ { "id": "test" }, "test_merged.geojson:md5,9fe55ab05e13024faee6daa2ddcf8e6d" ] + ], + "versions": [ + "versions.yml:md5,1d6e2b331dc05b3496a477c7e8adbeee", + "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", + "versions.yml:md5,74ae9680e8565f16244a79acbe2ef1e4" ] } ], @@ -34,7 +34,7 @@ "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2025-03-18T22:25:28.496236908" + "timestamp": "2025-03-19T09:25:50.356779643" }, "nuclear - tif - cellpose": { "content": [ @@ -52,18 +52,18 @@ "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", "versions.yml:md5,7e24ffbd0425ebf6bf537e55ac367001" ], - "versions": [ - "versions.yml:md5,1d6e2b331dc05b3496a477c7e8adbeee", - "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", - "versions.yml:md5,7e24ffbd0425ebf6bf537e55ac367001" - ], - "wkt": [ + "geojson": [ [ { "id": "test" }, "test_merged.geojson:md5,0d1072acebefc19c48bbcdb17ac57d5f" ] + ], + "versions": [ + "versions.yml:md5,1d6e2b331dc05b3496a477c7e8adbeee", + "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", + "versions.yml:md5,7e24ffbd0425ebf6bf537e55ac367001" ] } ], @@ -71,7 +71,7 @@ "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2025-03-18T22:24:29.505111421" + "timestamp": "2025-03-19T09:24:50.844367069" }, "nuclear - tif - deepcell": { "content": [ @@ -89,18 +89,18 @@ "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", "versions.yml:md5,e693a7e9c66cd7a37d9829cae2fc3648" ], - "versions": [ - "versions.yml:md5,1d6e2b331dc05b3496a477c7e8adbeee", - "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", - "versions.yml:md5,e693a7e9c66cd7a37d9829cae2fc3648" - ], - "wkt": [ + "geojson": [ [ { "id": "test" }, "test_merged.geojson:md5,a3f7237d662627863a30cff6128b989c" ] + ], + "versions": [ + "versions.yml:md5,1d6e2b331dc05b3496a477c7e8adbeee", + "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", + "versions.yml:md5,e693a7e9c66cd7a37d9829cae2fc3648" ] } ], @@ -108,7 +108,7 @@ "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2025-03-18T22:26:52.113552786" + "timestamp": "2025-03-19T09:27:14.541410552" }, "nuclear - tif - stardist": { "content": [ @@ -126,18 +126,18 @@ "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", "versions.yml:md5,e3945a4be7e4f9daa0ab9c717a9cce10" ], - "versions": [ - "versions.yml:md5,1d6e2b331dc05b3496a477c7e8adbeee", - "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", - "versions.yml:md5,e3945a4be7e4f9daa0ab9c717a9cce10" - ], - "wkt": [ + "geojson": [ [ { "id": "test" }, "test_merged.geojson:md5,590cf1b456fbae16631254f0f79121fc" ] + ], + "versions": [ + "versions.yml:md5,1d6e2b331dc05b3496a477c7e8adbeee", + "versions.yml:md5,4ca6951145ae8e8a22f95081060586e9", + "versions.yml:md5,e3945a4be7e4f9daa0ab9c717a9cce10" ] } ], @@ -145,6 +145,6 @@ "nf-test": "0.9.2", "nextflow": "24.04.4" }, - "timestamp": "2025-03-18T22:24:58.557258383" + "timestamp": "2025-03-19T09:25:19.772074638" } } \ No newline at end of file