From 7d6c36f111ee353c29fd36b420b0eda3dadf765c Mon Sep 17 00:00:00 2001 From: f641l Date: Fri, 24 Jul 2026 11:37:40 +0200 Subject: [PATCH 01/10] update xeniumranger import segemtnation --- .../nf-core/xeniumranger/import-segmentation/main.nf | 9 +++++++-- .../nf-core/xeniumranger/import-segmentation/meta.yml | 10 +++++++++- .../import-segmentation/tests/main.nf.test | 6 ++++-- 3 files changed, 20 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/xeniumranger/import-segmentation/main.nf b/modules/nf-core/xeniumranger/import-segmentation/main.nf index 0ecdcc0d1bb6..bb0980a6eaac 100644 --- a/modules/nf-core/xeniumranger/import-segmentation/main.nf +++ b/modules/nf-core/xeniumranger/import-segmentation/main.nf @@ -2,10 +2,10 @@ process XENIUMRANGER_IMPORT_SEGMENTATION { tag "$meta.id" label 'process_high' - container "quay.io/nf-core/xeniumranger:4.0" + container "nf-core/xeniumranger:4.0" input: - tuple val(meta), path(xenium_bundle, stageAs: "bundle/"), path(transcript_assignment), path(viz_polygons), path(nuclei), path(cells), path(coordinate_transform), val(units) + tuple val(meta), path(xenium_bundle, stageAs: "bundle/"), path(transcript_assignment), path(viz_polygons), path(nuclei), path(cells), path(coordinate_transform), val(units), val(expansion_distance) output: tuple val(meta), path("${prefix}"), emit: outs @@ -32,6 +32,11 @@ process XENIUMRANGER_IMPORT_SEGMENTATION { def assembled_args = [] if (task.ext.args) { assembled_args << task.ext.args.trim() } + // --expansion-distance is only valid for nuclei-based imports (it expands nuclei + // into cell boundaries). xeniumranger rejects it for transcript-assignment imports + // (proseg/baysor/segger) and cells-only imports with "--expansion-distance requires + // --nuclei", so only emit it when a nuclei segmentation is being imported. + if (nuclei && expansion_distance != null) { assembled_args << "--expansion-distance=${expansion_distance}" } if (nuclei) { assembled_args << "--nuclei=\"${nuclei}\"" } if (cells) { assembled_args << "--cells=\"${cells}\"" } if (transcript_assignment) { assembled_args << "--transcript-assignment=\"${transcript_assignment}\"" } diff --git a/modules/nf-core/xeniumranger/import-segmentation/meta.yml b/modules/nf-core/xeniumranger/import-segmentation/meta.yml index e222df582a05..0b29523e3e37 100644 --- a/modules/nf-core/xeniumranger/import-segmentation/meta.yml +++ b/modules/nf-core/xeniumranger/import-segmentation/meta.yml @@ -102,6 +102,14 @@ input: enum: - "microns" - "pixels" + - expansion_distance: + type: integer + optional: true + description: | + Distance (in microns) to expand nuclei outward into cell boundaries. Only valid for + nuclei-based imports (`nuclei` must be set); xeniumranger rejects it for + transcript-assignment imports and cells-only imports. Default: 5. Range: 0-100. + Passed to `--expansion-distance`. output: outs: - - meta: @@ -138,4 +146,4 @@ authors: - "@dongzehe" maintainers: - "@khersameesh24" - - "@dongzehe" + - "@dongzehe" \ No newline at end of file diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test index f85b8a7a0127..81677af00556 100644 --- a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test +++ b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test @@ -38,7 +38,8 @@ nextflow_process { bundle + "/cells.zarr.zip", [], [], - [] + [], + 5 ] } """ @@ -72,7 +73,8 @@ nextflow_process { bundle + "/cells.zarr.zip", [], [], - [] + [], + 5 ] } """ From 34bfa1bd0c5de15e35761d4e4de7e368997bbc94 Mon Sep 17 00:00:00 2001 From: f641l Date: Fri, 24 Jul 2026 11:45:55 +0200 Subject: [PATCH 02/10] correct container registry --- modules/nf-core/xeniumranger/import-segmentation/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/xeniumranger/import-segmentation/main.nf b/modules/nf-core/xeniumranger/import-segmentation/main.nf index bb0980a6eaac..eaf64ec3763d 100644 --- a/modules/nf-core/xeniumranger/import-segmentation/main.nf +++ b/modules/nf-core/xeniumranger/import-segmentation/main.nf @@ -2,7 +2,7 @@ process XENIUMRANGER_IMPORT_SEGMENTATION { tag "$meta.id" label 'process_high' - container "nf-core/xeniumranger:4.0" + container "quay.io/nf-core/xeniumranger:4.0" input: tuple val(meta), path(xenium_bundle, stageAs: "bundle/"), path(transcript_assignment), path(viz_polygons), path(nuclei), path(cells), path(coordinate_transform), val(units), val(expansion_distance) From 7f98762a86b9d8d2c3c7617f3451f3405f54825c Mon Sep 17 00:00:00 2001 From: f641l Date: Fri, 24 Jul 2026 12:07:34 +0200 Subject: [PATCH 03/10] changes to name and implmenet rec from matthias --- .../main.nf | 14 ++++++-------- .../meta.yml | 5 ++--- .../tests/main.nf.test | 4 ++-- .../tests/main.nf.test.snap | 12 ++++++------ 4 files changed, 16 insertions(+), 19 deletions(-) rename modules/nf-core/xeniumranger/{import-segmentation => importsegmentation}/main.nf (82%) rename modules/nf-core/xeniumranger/{import-segmentation => importsegmentation}/meta.yml (98%) rename modules/nf-core/xeniumranger/{import-segmentation => importsegmentation}/tests/main.nf.test (96%) rename modules/nf-core/xeniumranger/{import-segmentation => importsegmentation}/tests/main.nf.test.snap (81%) diff --git a/modules/nf-core/xeniumranger/import-segmentation/main.nf b/modules/nf-core/xeniumranger/importsegmentation/main.nf similarity index 82% rename from modules/nf-core/xeniumranger/import-segmentation/main.nf rename to modules/nf-core/xeniumranger/importsegmentation/main.nf index eaf64ec3763d..57ff2cb623c3 100644 --- a/modules/nf-core/xeniumranger/import-segmentation/main.nf +++ b/modules/nf-core/xeniumranger/importsegmentation/main.nf @@ -1,4 +1,4 @@ -process XENIUMRANGER_IMPORT_SEGMENTATION { +process XENIUMRANGER_IMPORTSEGMENTATION { tag "$meta.id" label 'process_high' @@ -18,7 +18,7 @@ process XENIUMRANGER_IMPORT_SEGMENTATION { // Exit if running this module with -profile conda / -profile mamba if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "XENIUMRANGER_IMPORT_SEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead." + error "XENIUMRANGER_IMPORTSEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead." } prefix = task.ext.prefix ?: "${meta.id}" @@ -32,10 +32,8 @@ process XENIUMRANGER_IMPORT_SEGMENTATION { def assembled_args = [] if (task.ext.args) { assembled_args << task.ext.args.trim() } - // --expansion-distance is only valid for nuclei-based imports (it expands nuclei - // into cell boundaries). xeniumranger rejects it for transcript-assignment imports - // (proseg/baysor/segger) and cells-only imports with "--expansion-distance requires - // --nuclei", so only emit it when a nuclei segmentation is being imported. + // --expansion-distance is only valid for nuclei-based imports. + // xeniumranger rejects it for transcript-assignment imports and cells-only imports. if (nuclei && expansion_distance != null) { assembled_args << "--expansion-distance=${expansion_distance}" } if (nuclei) { assembled_args << "--nuclei=\"${nuclei}\"" } if (cells) { assembled_args << "--cells=\"${cells}\"" } @@ -53,14 +51,14 @@ process XENIUMRANGER_IMPORT_SEGMENTATION { """ xeniumranger import-segmentation \\ - --id="XENIUMRANGER_IMPORT_SEGMENTATION" \\ + --id="XENIUMRANGER_IMPORTSEGMENTATION" \\ --xenium-bundle="${xenium_bundle}" \\ --localcores=${task.cpus} \\ --localmem=${task.memory.toGiga()} \\ ${args} rm -rf "${prefix}" - mv XENIUMRANGER_IMPORT_SEGMENTATION/outs "${prefix}" + mv XENIUMRANGER_IMPORTSEGMENTATION/outs "${prefix}" """ stub: diff --git a/modules/nf-core/xeniumranger/import-segmentation/meta.yml b/modules/nf-core/xeniumranger/importsegmentation/meta.yml similarity index 98% rename from modules/nf-core/xeniumranger/import-segmentation/meta.yml rename to modules/nf-core/xeniumranger/importsegmentation/meta.yml index 0b29523e3e37..e17e56de7fc2 100644 --- a/modules/nf-core/xeniumranger/import-segmentation/meta.yml +++ b/modules/nf-core/xeniumranger/importsegmentation/meta.yml @@ -1,4 +1,4 @@ -name: xeniumranger_import_segmentation +name: XENIUMRANGER_IMPORTSEGMENTATION description: | The xeniumranger import-segmentation module runs `xeniumranger import-segmentation` to recompute Xenium Onboard Analysis outputs using external segmentation results. @@ -108,8 +108,7 @@ input: description: | Distance (in microns) to expand nuclei outward into cell boundaries. Only valid for nuclei-based imports (`nuclei` must be set); xeniumranger rejects it for - transcript-assignment imports and cells-only imports. Default: 5. Range: 0-100. - Passed to `--expansion-distance`. + transcript-assignment imports and cells-only imports. Default: 5. Range: 0-100. output: outs: - - meta: diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test similarity index 96% rename from modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test rename to modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test index 81677af00556..3daaf93a0708 100644 --- a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test @@ -1,8 +1,8 @@ nextflow_process { - name "Test Process XENIUMRANGER_IMPORT_SEGMENTATION" + name "Test Process XENIUMRANGER_IMPORTSEGMENTATION" script "../main.nf" - process "XENIUMRANGER_IMPORT_SEGMENTATION" + process "XENIUMRANGER_IMPORTSEGMENTATION" tag "modules" tag "modules_nfcore" diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap similarity index 81% rename from modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap rename to modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap index 337133b2777d..871f33328193 100644 --- a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap @@ -12,17 +12,17 @@ ], "versions_xeniumranger": [ [ - "XENIUMRANGER_IMPORT_SEGMENTATION", + "XENIUMRANGER_IMPORTSEGMENTATION", "xeniumranger", "4.0.1.1" ] ] } ], - "timestamp": "2026-06-16T05:59:47.015555128", + "timestamp": "2026-07-24T12:06:39.971558886", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.0" + "nextflow": "26.04.6" } }, "xeniumranger import-segmentation stub": { @@ -40,17 +40,17 @@ ], "versions_xeniumranger": [ [ - "XENIUMRANGER_IMPORT_SEGMENTATION", + "XENIUMRANGER_IMPORTSEGMENTATION", "xeniumranger", "4.0.1.1" ] ] } ], - "timestamp": "2026-06-16T05:59:56.522779629", + "timestamp": "2026-07-24T12:06:52.922050231", "meta": { "nf-test": "0.9.5", - "nextflow": "26.04.0" + "nextflow": "26.04.6" } } } \ No newline at end of file From 27677c0e10d512844d608ed55c57a2eb6dfcc03d Mon Sep 17 00:00:00 2001 From: f641l Date: Fri, 24 Jul 2026 12:18:28 +0200 Subject: [PATCH 04/10] made a msitake --- .github/skip_nf_test.json | 2 +- .../xeniumranger/importsegmentation/meta.yml | 2 +- .../importsegmentation/tests/main.nf.test | 10 ++-- .../tests/main.nf.test.snap | 54 +++++++++++++++++++ 4 files changed, 61 insertions(+), 7 deletions(-) diff --git a/.github/skip_nf_test.json b/.github/skip_nf_test.json index 1f94d6a31cbe..50d489477088 100644 --- a/.github/skip_nf_test.json +++ b/.github/skip_nf_test.json @@ -107,7 +107,7 @@ "modules/nf-core/universc", "modules/nf-core/vt/decompose", "modules/nf-core/wittyer", - "modules/nf-core/xeniumranger/import-segmentation", + "modules/nf-core/xeniumranger/importsegmentation", "modules/nf-core/xeniumranger/relabel", "modules/nf-core/xeniumranger/rename", "modules/nf-core/xeniumranger/resegment", diff --git a/modules/nf-core/xeniumranger/importsegmentation/meta.yml b/modules/nf-core/xeniumranger/importsegmentation/meta.yml index e17e56de7fc2..9f23de45c536 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/meta.yml +++ b/modules/nf-core/xeniumranger/importsegmentation/meta.yml @@ -1,6 +1,6 @@ name: XENIUMRANGER_IMPORTSEGMENTATION description: | - The xeniumranger import-segmentation module runs `xeniumranger import-segmentation` + The xeniumranger importsegmentation module runs `xeniumranger import-segmentation` to recompute Xenium Onboard Analysis outputs using external segmentation results. It supports two execution modes mirroring the Xenium Ranger CLI: an image-based mode that accepts nuclei and/or cell masks (TIFF/NPY) or GeoJSON polygons together diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test index 3daaf93a0708..cc255215fe1b 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test @@ -7,7 +7,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "xeniumranger" - tag "xeniumranger/import-segmentation" + tag "xeniumranger/importsegmentation" tag "unzip" @@ -24,14 +24,14 @@ nextflow_process { } - test("xeniumranger import-segmentation nuclei") { + test("xeniumranger importsegmentation nuclei") { when { process { """ input[0] = UNZIP.out.unzipped_archive .map { meta, bundle -> [ - [id: "test_xeniumranger_import-segmentation"], + [id: "test_xeniumranger_importsegmentation"], bundle, [], [], @@ -57,7 +57,7 @@ nextflow_process { } } - test("xeniumranger import-segmentation stub") { + test("xeniumranger importsegmentation stub") { options "-stub" when { @@ -66,7 +66,7 @@ nextflow_process { input[0] = UNZIP.out.unzipped_archive .map { meta, bundle -> [ - [id: "test_xeniumranger_import-segmentation"], + [id: "test_xeniumranger_importsegmentation"], bundle, [], [], diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap index 871f33328193..6a8711c5f746 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap @@ -52,5 +52,59 @@ "nf-test": "0.9.5", "nextflow": "26.04.6" } + }, + "xeniumranger importsegmentation stub": { + "content": [ + { + "outs": [ + [ + { + "id": "test_xeniumranger_importsegmentation" + }, + [ + "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions_xeniumranger": [ + [ + "XENIUMRANGER_IMPORTSEGMENTATION", + "xeniumranger", + "4.0.1.1" + ] + ] + } + ], + "timestamp": "2026-07-24T12:17:40.330610992", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } + }, + "xeniumranger importsegmentation nuclei": { + "content": [ + { + "outs": [ + [ + { + "id": "test_xeniumranger_importsegmentation" + }, + "test_xeniumranger_importsegmentation" + ] + ], + "versions_xeniumranger": [ + [ + "XENIUMRANGER_IMPORTSEGMENTATION", + "xeniumranger", + "4.0.1.1" + ] + ] + } + ], + "timestamp": "2026-07-24T12:17:23.188617665", + "meta": { + "nf-test": "0.9.5", + "nextflow": "26.04.6" + } } } \ No newline at end of file From 327d8c5b285946a375ef739615359f788c1fe313 Mon Sep 17 00:00:00 2001 From: f641l Date: Fri, 24 Jul 2026 14:37:34 +0200 Subject: [PATCH 05/10] update snap --- .../tests/main.nf.test.snap | 58 +------------------ 1 file changed, 2 insertions(+), 56 deletions(-) diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap index 6a8711c5f746..c574cb16aaff 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap @@ -1,58 +1,4 @@ { - "xeniumranger import-segmentation nuclei": { - "content": [ - { - "outs": [ - [ - { - "id": "test_xeniumranger_import-segmentation" - }, - "test_xeniumranger_import-segmentation" - ] - ], - "versions_xeniumranger": [ - [ - "XENIUMRANGER_IMPORTSEGMENTATION", - "xeniumranger", - "4.0.1.1" - ] - ] - } - ], - "timestamp": "2026-07-24T12:06:39.971558886", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" - } - }, - "xeniumranger import-segmentation stub": { - "content": [ - { - "outs": [ - [ - { - "id": "test_xeniumranger_import-segmentation" - }, - [ - "experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ] - ], - "versions_xeniumranger": [ - [ - "XENIUMRANGER_IMPORTSEGMENTATION", - "xeniumranger", - "4.0.1.1" - ] - ] - } - ], - "timestamp": "2026-07-24T12:06:52.922050231", - "meta": { - "nf-test": "0.9.5", - "nextflow": "26.04.6" - } - }, "xeniumranger importsegmentation stub": { "content": [ { @@ -75,7 +21,7 @@ ] } ], - "timestamp": "2026-07-24T12:17:40.330610992", + "timestamp": "2026-07-24T14:37:06.226798831", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" @@ -101,7 +47,7 @@ ] } ], - "timestamp": "2026-07-24T12:17:23.188617665", + "timestamp": "2026-07-24T14:36:51.425534108", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" From 6cf4748bcf024ae30e36281760c620c427dd9185 Mon Sep 17 00:00:00 2001 From: f641l Date: Mon, 27 Jul 2026 11:28:45 +0200 Subject: [PATCH 06/10] switching to smaller test data --- .../xeniumranger/importsegmentation/tests/main.nf.test | 10 +++++----- .../importsegmentation/tests/main.nf.test.snap | 4 ++-- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test index cc255215fe1b..073db07ff420 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test @@ -13,11 +13,11 @@ nextflow_process { setup { - run("UNZIP") { - script "modules/nf-core/unzip/main.nf" + run("UNTAR") { + script "modules/nf-core/untar/main.nf" process { """ - input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip', checkIfExists: true)] + input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialaxe/xenium_bundle.tar.gz', checkIfExists: true)] """ } } @@ -28,7 +28,7 @@ nextflow_process { when { process { """ - input[0] = UNZIP.out.unzipped_archive + input[0] = UNTAR.out.untar .map { meta, bundle -> [ [id: "test_xeniumranger_importsegmentation"], @@ -63,7 +63,7 @@ nextflow_process { when { process { """ - input[0] = UNZIP.out.unzipped_archive + input[0] = UNTAR.out.untar .map { meta, bundle -> [ [id: "test_xeniumranger_importsegmentation"], diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap index c574cb16aaff..c0a15509071d 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] } ], - "timestamp": "2026-07-24T14:37:06.226798831", + "timestamp": "2026-07-27T11:22:26.133922915", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" @@ -47,7 +47,7 @@ ] } ], - "timestamp": "2026-07-24T14:36:51.425534108", + "timestamp": "2026-07-27T11:22:18.825694797", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" From e2534bcc254b1810f6f388b970519cb9c4e6da21 Mon Sep 17 00:00:00 2001 From: f641l Date: Mon, 27 Jul 2026 11:38:11 +0200 Subject: [PATCH 07/10] fix missing tag --- .../xeniumranger/importsegmentation/tests/main.nf.test | 2 +- .../xeniumranger/importsegmentation/tests/main.nf.test.snap | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test index 073db07ff420..f28a26fdd04e 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "modules_nfcore" tag "xeniumranger" tag "xeniumranger/importsegmentation" - tag "unzip" + tag "untar" setup { diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap index c0a15509071d..aa5c121a20b7 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] } ], - "timestamp": "2026-07-27T11:22:26.133922915", + "timestamp": "2026-07-27T11:37:59.190980105", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" @@ -47,7 +47,7 @@ ] } ], - "timestamp": "2026-07-27T11:22:18.825694797", + "timestamp": "2026-07-27T11:37:49.642076574", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" From 915bbaf722cc5ffa400a1f5426c15e84ed9c8413 Mon Sep 17 00:00:00 2001 From: f641l Date: Mon, 27 Jul 2026 15:07:04 +0200 Subject: [PATCH 08/10] adding nextflow.config --- .../importsegmentation/tests/main.nf.test.snap | 4 ++-- .../xeniumranger/importsegmentation/tests/nextflow.config | 7 +++++++ 2 files changed, 9 insertions(+), 2 deletions(-) create mode 100644 modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap index aa5c121a20b7..7fb4365541e2 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] } ], - "timestamp": "2026-07-27T11:37:59.190980105", + "timestamp": "2026-07-27T15:02:26.958198169", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" @@ -47,7 +47,7 @@ ] } ], - "timestamp": "2026-07-27T11:37:49.642076574", + "timestamp": "2026-07-27T15:02:12.93562615", "meta": { "nf-test": "0.9.5", "nextflow": "26.04.6" diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config b/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config new file mode 100644 index 000000000000..c273683ba5a6 --- /dev/null +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + resourceLimits = [ + cpus: 2 + ] + +} \ No newline at end of file From 07f38472e74ffd2605ee105821345ed8cb097e58 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 27 Jul 2026 16:13:33 +0200 Subject: [PATCH 09/10] Apply suggestion from @mashehu --- .../xeniumranger/importsegmentation/tests/nextflow.config | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config b/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config index c273683ba5a6..b1a97a30e4c0 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config @@ -1,7 +1,6 @@ process { - resourceLimits = [ - cpus: 2 - ] - + withName:XENIUMRANGER_IMPORTSEGMENTATION { + cpus = 2 + } } \ No newline at end of file From 7e958502503719669b711b6d88ead5f7a7445256 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 27 Jul 2026 21:35:57 +0200 Subject: [PATCH 10/10] limit cpu, memory and time and import config --- .../importsegmentation/tests/main.nf.test | 1 + .../importsegmentation/tests/nextflow.config | 11 ++++++----- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test index f28a26fdd04e..1510df320e04 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process XENIUMRANGER_IMPORTSEGMENTATION" script "../main.nf" process "XENIUMRANGER_IMPORTSEGMENTATION" + config "./nextflow.config" tag "modules" tag "modules_nfcore" diff --git a/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config b/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config index b1a97a30e4c0..39b095f8b2ba 100644 --- a/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config +++ b/modules/nf-core/xeniumranger/importsegmentation/tests/nextflow.config @@ -1,6 +1,7 @@ process { - - withName:XENIUMRANGER_IMPORTSEGMENTATION { - cpus = 2 - } -} \ No newline at end of file + withName: XENIUMRANGER_IMPORTSEGMENTATION { + cpus = 2 + memory = '4.GB' + time = '30.m' + } +}