From 94e0e36c28c18b956b8f51b6d7d23aa9f13564c3 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Wed, 27 Aug 2025 12:47:41 +0200 Subject: [PATCH 01/27] update pipeline level test --- nf-test.config | 2 +- tests/default.nf.test | 4 +- tests/default.nf.test.snap | 576 +++++++++++++++++++++++++++++++++++++ tests/preprocess.nf.test | 3 +- 4 files changed, 582 insertions(+), 3 deletions(-) create mode 100644 tests/default.nf.test.snap diff --git a/nf-test.config b/nf-test.config index 604f3b6..2285cf7 100644 --- a/nf-test.config +++ b/nf-test.config @@ -12,7 +12,7 @@ config { ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*' // run all test with defined profile(s) from the main nextflow.config - profile "test, docker" + profile "docker" // list of filenames or patterns that should be trigger a full test run triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore' diff --git a/tests/default.nf.test b/tests/default.nf.test index e24f22d..13668ea 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -3,8 +3,10 @@ nextflow_pipeline { name "Test pipeline" script "../main.nf" tag "pipeline" + tag "gpu" + profile "docker,test_gpu" - test("-profile test") { + test("-profile test_gpu") { when { params { diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap new file mode 100644 index 0000000..cc440cd --- /dev/null +++ b/tests/default.nf.test.snap @@ -0,0 +1,576 @@ +{ + "-profile test_gpu": { + "content": [ + 8, + { + "MAT2JSON_INT": { + "mat2json": 1.0 + }, + "NUMORPH3DUNET": { + "numorph3dunet": 1.0 + }, + "NUMORPHALIGN": { + "numorphalign": 1.0 + }, + "NUMORPHINTENSITY": { + "numorphintensity": 1.0 + }, + "NUMORPHSTITCH": { + "numorphstitch": 1.0 + }, + "UNZIP": { + "7za": 16.02 + }, + "Workflow": { + "nf-core/lsmquant": "v1.0dev" + } + }, + [ + "TEST1", + "TEST1/alignment", + "TEST1/alignment/results", + "TEST1/alignment/results/NM_variables.mat", + "TEST1/alignment/results/samples", + "TEST1/alignment/results/samples/alignment", + "TEST1/alignment/results/samples/alignment/TEST1_ctip2_full.tif", + "TEST1/alignment/results/samples/alignment/TEST1_topro_full.tif", + "TEST1/alignment/results/variables", + "TEST1/alignment/results/variables/alignment_table.mat", + "TEST1/alignment/results/variables/path_table.mat", + "TEST1/alignment/results/variables/z_displacement_align.mat", + "TEST1/intensity", + "TEST1/intensity/results", + "TEST1/intensity/results/NM_variables.mat", + "TEST1/intensity/results/samples", + "TEST1/intensity/results/samples/intensity_adjustment", + "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_1_11.tif", + "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_2_11.tif", + "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_1_11.tif", + "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_2_11.tif", + "TEST1/intensity/results/samples/intensity_adjustment/flatfield_1.png", + "TEST1/intensity/results/samples/intensity_adjustment/flatfield_2.png", + "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_1.png", + "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_2.png", + "TEST1/intensity/results/samples/intensity_adjustment/topro_1_1_11.tif", + "TEST1/intensity/results/samples/intensity_adjustment/topro_1_2_11.tif", + "TEST1/intensity/results/samples/intensity_adjustment/topro_2_1_11.tif", + "TEST1/intensity/results/samples/intensity_adjustment/topro_2_2_11.tif", + "TEST1/intensity/results/samples/intensity_adjustment/y_adj_1.png", + "TEST1/intensity/results/samples/intensity_adjustment/y_adj_2.png", + "TEST1/intensity/results/variables", + "TEST1/intensity/results/variables/adj_params.mat", + "TEST1/intensity/results/variables/path_table.mat", + "TEST1/intensity/results/variables/thresholds.mat", + "TEST1/mat2json", + "TEST1/mat2json/align", + "TEST1/mat2json/align/NM_variables.json", + "TEST1/mat2json/align/alignment_table.json", + "TEST1/mat2json/align/path_table.json", + "TEST1/mat2json/align/z_displacement_align.json", + "TEST1/mat2json/intensity", + "TEST1/mat2json/intensity/NM_variables.json", + "TEST1/mat2json/intensity/adj_params.json", + "TEST1/mat2json/intensity/path_table.json", + "TEST1/mat2json/intensity/thresholds.json", + "TEST1/mat2json/stitch", + "TEST1/mat2json/stitch/adj_params.json", + "TEST1/mat2json/stitch/adjusted_z.csv", + "TEST1/mat2json/stitch/alignment_table.json", + "TEST1/mat2json/stitch/path_table.json", + "TEST1/mat2json/stitch/stitch_tforms.json", + "TEST1/mat2json/stitch/thresholds.json", + "TEST1/mat2json/stitch/z_disp_matrix.json", + "TEST1/mat2json/stitch/z_displacement_align.json", + "TEST1/mat2json/versions.yml", + "TEST1/segmentation", + "TEST1/segmentation/TEST1.csv", + "TEST1/segmentation/TEST1_counts.csv", + "TEST1/stitching", + "TEST1/stitching/results", + "TEST1/stitching/results/NM_variables.mat", + "TEST1/stitching/results/stitched", + "TEST1/stitching/results/stitched/TEST1_0001_C1_topro_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0001_C2_ctip2_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0002_C1_topro_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0002_C2_ctip2_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0003_C1_topro_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0003_C2_ctip2_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0004_C1_topro_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0004_C2_ctip2_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0005_C1_topro_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0005_C2_ctip2_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0006_C1_topro_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0006_C2_ctip2_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0007_C1_topro_stitched.tif", + "TEST1/stitching/results/stitched/TEST1_0007_C2_ctip2_stitched.tif", + 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Z0610.ome.tif:md5,486dad8db46e853eee60dccfc716b543", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0611.ome.tif:md5,3a4caf7fab942a5eb0a8666a86c4552e", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0612.ome.tif:md5,7781ff916dfae4f9b8093d04d2e5ddd6", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0613.ome.tif:md5,93269be5f9ba1e07b2ee253f9f9574d9", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0614.ome.tif:md5,013f6d3ea185745eb2e02c05f3418eaf", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0615.ome.tif:md5,c59a5b5dd08bf4acfa0f954e25c5419f", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0616.ome.tif:md5,9b122cba54fb3d8f2f3f7a9df7b9821b", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0617.ome.tif:md5,fa8f8bef57029e14c0eb6daf7bab2886", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0618.ome.tif:md5,d316f89e3752621cb93bf8de1f694000", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0619.ome.tif:md5,43d0386b21d9f6a36c209dc3ab60d1cc", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0620.ome.tif:md5,b4f4be8e38b3b84dcd1a34a2b1968abc" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-08-27T12:44:17.082585224" + } +} \ No newline at end of file diff --git a/tests/preprocess.nf.test b/tests/preprocess.nf.test index f0fab75..533fada 100644 --- a/tests/preprocess.nf.test +++ b/tests/preprocess.nf.test @@ -4,8 +4,9 @@ nextflow_pipeline { script "../main.nf" tag "cpu" tag "pipeline_lsmquant" + profile "test" - test("-profile test") { + test("-profile test preprocess") { when { params { From ab0542df6f9edcfded2532e569d2da4e582e5e5e Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Wed, 27 Aug 2025 13:55:51 +0200 Subject: [PATCH 02/27] update subworkflows + modules, update meta.yml of numorph subworkflows --- modules.json | 12 ++-- modules/nf-core/basicpy/environment.yml | 3 - modules/nf-core/basicpy/main.nf | 15 +++-- modules/nf-core/basicpy/meta.yml | 27 +++++--- modules/nf-core/basicpy/tests/main.nf.test | 64 +++++++++++++++++++ .../nf-core/basicpy/tests/main.nf.test.snap | 53 +++++++++++++++ modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +- modules/nf-core/multiqc/meta.yml | 0 modules/nf-core/multiqc/tests/main.nf.test | 0 .../nf-core/multiqc/tests/main.nf.test.snap | 20 +++--- modules/nf-core/multiqc/tests/tags.yml | 2 - modules/nf-core/unzip/meta.yml | 18 ++++-- modules/nf-core/unzip/tests/tags.yml | 2 - subworkflows/local/araregistration/meta.yml | 59 +++++++++-------- .../local/numorph_preprocessing/main.nf | 2 +- .../local/numorph_preprocessing/meta.yml | 57 ++++++++--------- .../nf-core/utils_nextflow_pipeline/main.nf | 0 .../nf-core/utils_nextflow_pipeline/meta.yml | 0 .../tests/main.function.nf.test | 0 .../tests/main.function.nf.test.snap | 0 .../tests/main.workflow.nf.test | 0 .../tests/nextflow.config | 0 .../utils_nextflow_pipeline/tests/tags.yml | 2 - .../nf-core/utils_nfcore_pipeline/main.nf | 0 .../nf-core/utils_nfcore_pipeline/meta.yml | 0 .../tests/main.function.nf.test | 0 .../tests/main.function.nf.test.snap | 0 .../tests/main.workflow.nf.test | 0 .../tests/main.workflow.nf.test.snap | 0 .../tests/nextflow.config | 0 .../utils_nfcore_pipeline/tests/tags.yml | 2 - .../tests/nextflow.config | 2 +- .../tests/nextflow_schema.json | 0 34 files changed, 234 insertions(+), 112 deletions(-) delete mode 100644 modules/nf-core/basicpy/environment.yml create mode 100644 modules/nf-core/basicpy/tests/main.nf.test create mode 100644 modules/nf-core/basicpy/tests/main.nf.test.snap mode change 100755 => 100644 modules/nf-core/multiqc/environment.yml mode change 100755 => 100644 modules/nf-core/multiqc/main.nf mode change 100755 => 100644 modules/nf-core/multiqc/meta.yml mode change 100755 => 100644 modules/nf-core/multiqc/tests/main.nf.test mode change 100755 => 100644 modules/nf-core/multiqc/tests/main.nf.test.snap delete mode 100755 modules/nf-core/multiqc/tests/tags.yml delete mode 100644 modules/nf-core/unzip/tests/tags.yml mode change 100755 => 100644 subworkflows/nf-core/utils_nextflow_pipeline/main.nf mode change 100755 => 100644 subworkflows/nf-core/utils_nextflow_pipeline/meta.yml mode change 100755 => 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test mode change 100755 => 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap mode change 100755 => 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test mode change 100755 => 100644 subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config delete mode 100755 subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml mode change 100755 => 100644 subworkflows/nf-core/utils_nfcore_pipeline/main.nf mode change 100755 => 100644 subworkflows/nf-core/utils_nfcore_pipeline/meta.yml mode change 100755 => 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test mode change 100755 => 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap mode change 100755 => 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test mode change 100755 => 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap mode change 100755 => 100644 subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config delete mode 100755 subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml mode change 100755 => 100644 subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json diff --git a/modules.json b/modules.json index e780646..6c05a02 100755 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "basicpy": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "fastqc": { @@ -17,12 +17,12 @@ }, "multiqc": { "branch": "master", - "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", + "git_sha": "a4488d3d09244f29fb4606ba4eef85d59dcc6ad8", "installed_by": ["modules"] }, "unzip": { "branch": "master", - "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc", + "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46", "installed_by": ["modules"] }, "unzipfiles": { @@ -36,17 +36,17 @@ "nf-core": { "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b", + "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a", + "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", - "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e", + "git_sha": "dcd088f483cede0c3df4034d405126f05a764cc7", "installed_by": ["subworkflows"] } } diff --git a/modules/nf-core/basicpy/environment.yml b/modules/nf-core/basicpy/environment.yml deleted file mode 100644 index 3cebeff..0000000 --- a/modules/nf-core/basicpy/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: - - conda-forge - - bioconda diff --git a/modules/nf-core/basicpy/main.nf b/modules/nf-core/basicpy/main.nf index da87a0b..7cf650f 100644 --- a/modules/nf-core/basicpy/main.nf +++ b/modules/nf-core/basicpy/main.nf @@ -8,8 +8,8 @@ process BASICPY { tuple val(meta), path(image) output: - tuple val(meta), path("*.tiff"), emit: fields - path "versions.yml" , emit: versions + tuple val(meta), path("*-dfp.tiff"), path("*-ffp.tiff"), emit: profiles + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -19,15 +19,14 @@ process BASICPY { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "Basicpy module does not support Conda. Please use Docker / Singularity instead." } - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' def VERSION = "1.2.0-patch1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping """ /opt/main.py -i $image -o . $args cat <<-END_VERSIONS > versions.yml "${task.process}": - basicpy:: $VERSION + basicpy: $VERSION END_VERSIONS """ @@ -36,13 +35,15 @@ process BASICPY { if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { error "Basicpy module does not support Conda. Please use Docker / Singularity instead." } + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = "1.2.0-patch1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping """ touch ${prefix}.-dfp.tiff - touch ${prefix}.-dfp.tiff + touch ${prefix}.-ffp.tiff cat <<-END_VERSIONS > versions.yml "${task.process}": - basicpy:: $VERSION + basicpy: $VERSION END_VERSIONS """ } diff --git a/modules/nf-core/basicpy/meta.yml b/modules/nf-core/basicpy/meta.yml index b143f5d..2cdd992 100644 --- a/modules/nf-core/basicpy/meta.yml +++ b/modules/nf-core/basicpy/meta.yml @@ -28,22 +28,31 @@ input: type: file description: Tiff file to be used for dark and flat field illumination correction pattern: "*.{tiff,tif}" + ontologies: [] output: - - fields: - - meta: + profiles: + - - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test' ] - - "*.tiff": + - "*-dfp.tiff": type: file - description: Tiff fields for dark and flat field illumination correction - pattern: "*.{tiff,tif}" - - versions: - - versions.yml: + description: Tiff fields for dark field illumination correction + pattern: "*.{tiff}" + ontologies: [] + - "*-ffp.tiff": type: file - description: File containing software versions - pattern: "versions.yml" + description: Tiff fields for flat field illumination correction + pattern: "*.{tiff}" + ontologies: [] + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/basicpy/tests/main.nf.test b/modules/nf-core/basicpy/tests/main.nf.test new file mode 100644 index 0000000..40ba4dd --- /dev/null +++ b/modules/nf-core/basicpy/tests/main.nf.test @@ -0,0 +1,64 @@ +nextflow_process { + + name "Test Process BASICPY" + script "../main.nf" + process "BASICPY" + + tag "modules" + tag "modules_nfcore" + tag "basicpy" + + test("basicpy - OME-TIFF") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.profiles.get(0).get(1)).exists(), + file(process.out.profiles.get(0).get(2)).exists(), + file(process.out.profiles.get(0).get(1)).size(), + file(process.out.profiles.get(0).get(2)).size() + ).match() + }, + ) + } + + } + + test("basicpy - OME-TIFF - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'imaging/ome-tiff/cycif-tonsil-cycle1.ome.tif', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/basicpy/tests/main.nf.test.snap b/modules/nf-core/basicpy/tests/main.nf.test.snap new file mode 100644 index 0000000..94b14ec --- /dev/null +++ b/modules/nf-core/basicpy/tests/main.nf.test.snap @@ -0,0 +1,53 @@ +{ + "basicpy - OME-TIFF": { + "content": [ + [ + "versions.yml:md5,1391fd5a5745a20016f9824467273113" + ], + true, + true, + 633904, + 633904 + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-03-12T20:14:46.041882924" + }, + "basicpy - OME-TIFF - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.-dfp.tiff:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.-ffp.tiff:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,1391fd5a5745a20016f9824467273113" + ], + "profiles": [ + [ + { + "id": "test" + }, + "test.-dfp.tiff:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.-ffp.tiff:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,1391fd5a5745a20016f9824467273113" + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-03-12T20:14:53.621168198" + } +} \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml old mode 100755 new mode 100644 index 812fc4c..f893704 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.29 + - bioconda::multiqc=1.30 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf old mode 100755 new mode 100644 index 0ac3c36..67460de --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.29--pyhdfd78af_0' : - 'biocontainers/multiqc:1.29--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.30--pyhdfd78af_1' : + 'biocontainers/multiqc:1.30--pyhdfd78af_1' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml old mode 100755 new mode 100644 diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test old mode 100755 new mode 100644 diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap old mode 100755 new mode 100644 index 88e9057..0d3f288 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,e65ce731db2128b8e4dd43d6e880fc1c" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-22T11:50:41.182332996" + "timestamp": "2025-07-10T08:06:23.563041241" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,e65ce731db2128b8e4dd43d6e880fc1c" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-22T11:51:22.448739369" + "timestamp": "2025-07-10T08:06:48.96226832" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,c1fe644a37468f6dae548d98bc72c2c1" + "versions.yml:md5,e65ce731db2128b8e4dd43d6e880fc1c" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.2" + "nextflow": "25.04.3" }, - "timestamp": "2025-05-22T11:51:06.198928424" + "timestamp": "2025-07-10T08:06:40.627008706" } -} \ No newline at end of file +} diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100755 index bea6c0d..0000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/modules/nf-core/unzip/meta.yml b/modules/nf-core/unzip/meta.yml index 426fccb..ba1eb91 100644 --- a/modules/nf-core/unzip/meta.yml +++ b/modules/nf-core/unzip/meta.yml @@ -24,9 +24,11 @@ input: type: file description: ZIP file pattern: "*.zip" + ontologies: + - edam: http://edamontology.org/format_3987 # ZIP format output: - - unzipped_archive: - - meta: + unzipped_archive: + - - meta: type: map description: | Groovy Map containing sample information @@ -35,11 +37,13 @@ output: type: directory description: Directory contents of the unzipped archive pattern: "${archive.baseName}/" - - versions: - - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/unzip/tests/tags.yml b/modules/nf-core/unzip/tests/tags.yml deleted file mode 100644 index 7f5647e..0000000 --- a/modules/nf-core/unzip/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -unzip: - - "modules/nf-core/unzip/**" diff --git a/subworkflows/local/araregistration/meta.yml b/subworkflows/local/araregistration/meta.yml index 4da8bc7..36d04c2 100644 --- a/subworkflows/local/araregistration/meta.yml +++ b/subworkflows/local/araregistration/meta.yml @@ -1,44 +1,47 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json name: "araregistration" ## TODO nf-core: Add a description of the subworkflow and list keywords -description: Sort SAM/BAM/CRAM file +description: Image registration of 2D stitched images to the Allan reference atlas keywords: - - sort - - bam - - sam - - cram -## TODO nf-core: Add a list of the modules and/or subworkflows used in the subworkflow + - registration + - mouse brain + - atlas components: - - samtools/sort - - samtools/index -## TODO nf-core: List all of the channels used as input with a description and their structure + - numorphresample + - numorphregister + - mat2json input: - - ch_bam: - type: file + - stitched_data: + type: path + description: | + The input channel containing the stitched TIFF files and the parameter file + Structure: [ val(meta), path(stitched), path(parameters) ] + pattern: "*.tif/tiff/csv" + - NM_variables: + type: path description: | - The input channel containing the BAM/CRAM/SAM files - Structure: [ val(meta), path(bam) ] - pattern: "*.{bam/cram/sam}" -## TODO nf-core: List all of the channels used as output with a descriptions and their structure + The input channel containing the numorph processing parameter file (MAT) + Structure: [ val(meta), path(NM_variables) ] + pattern: "*.mat" output: - - bam: + - reg_mask: type: file description: | - Channel containing BAM files - Structure: [ val(meta), path(bam) ] - pattern: "*.bam" - - bai: - type: file + Channel containing registration mask file + Structure: path(mat) + pattern: "*.mat" + - registered: + type: path description: | - Channel containing indexed BAM (BAI) files - Structure: [ val(meta), path(bai) ] - pattern: "*.bai" - - csi: + Channel containing path to registered image files + Structure: path(nii) + pattern: "*.nii" + - NM_variables: type: file description: | - Channel containing CSI files - Structure: [ val(meta), path(csi) ] - pattern: "*.csi" + Channel containing numorph processing parameter file (MAT) + Structure: path(NM_variables.mat) + pattern: "*.mat" - versions: type: file description: | diff --git a/subworkflows/local/numorph_preprocessing/main.nf b/subworkflows/local/numorph_preprocessing/main.nf index af503ce..66e9412 100644 --- a/subworkflows/local/numorph_preprocessing/main.nf +++ b/subworkflows/local/numorph_preprocessing/main.nf @@ -9,7 +9,7 @@ include { MAT2JSON as MAT2JSON_STITCH } from '../../../modules/local/ma workflow NUMORPH_PREPROCESSING { take: - samplesheet // channel: [ val(meta), path(imf_directory), path(parameter_file) ] + samplesheet // channel: [ val(meta), path(img_directory), path(parameter_file) ] main: diff --git a/subworkflows/local/numorph_preprocessing/meta.yml b/subworkflows/local/numorph_preprocessing/meta.yml index 7cff8b8..badc35d 100644 --- a/subworkflows/local/numorph_preprocessing/meta.yml +++ b/subworkflows/local/numorph_preprocessing/meta.yml @@ -1,44 +1,43 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json name: "numorph_preprocessing" -## TODO nf-core: Add a description of the subworkflow and list keywords -description: Sort SAM/BAM/CRAM file +description: preprocessing (intensity adjustment, alignment, stitching) of 2D single channel single tile TIFF images. keywords: - - sort - - bam - - sam - - cram -## TODO nf-core: Add a list of the modules and/or subworkflows used in the subworkflow + - intensity + - alignment + - stitching + - tiff + components: - - samtools/sort - - samtools/index -## TODO nf-core: List all of the channels used as input with a description and their structure + - numorphintensity + - numorphalign + - numorphstitch + - mat2json input: - - ch_bam: - type: file + - samplesheet: + type: tuple description: | - The input channel containing the BAM/CRAM/SAM files - Structure: [ val(meta), path(bam) ] - pattern: "*.{bam/cram/sam}" -## TODO nf-core: List all of the channels used as output with a descriptions and their structure + The input channel containing the metadata, image directory and parameter file. + Structure: [ val(meta), path(img_directory), path(parameter_file)] + pattern: "*.{tif/tiff/csv}" output: - - bam: - type: file + - stitched: + type: path description: | - Channel containing BAM files - Structure: [ val(meta), path(bam) ] - pattern: "*.bam" - - bai: + Channel containing path to stitched Tiff files + Structure: [ val(meta), path(stitched) ] + pattern: "*.tif/tiff" + - intensity_thresholds: type: file description: | - Channel containing indexed BAM (BAI) files - Structure: [ val(meta), path(bai) ] - pattern: "*.bai" - - csi: + Channel containing intensity threshold (MAT) file + Structure: path(thresholds_mat) + pattern: "*.mat" + - NM_variables: type: file description: | - Channel containing CSI files - Structure: [ val(meta), path(csi) ] - pattern: "*.csi" + Channel containing numorph processing parameter file (MAT) + Structure: path(NM_variables.mat) + pattern: "*.mat" - versions: type: file description: | diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml b/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.function.nf.test.snap old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nextflow_pipeline/tests/main.workflow.nf.test old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml deleted file mode 100755 index f847611..0000000 --- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nextflow_pipeline: - - subworkflows/nf-core/utils_nextflow_pipeline/** diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml b/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.function.nf.test.snap old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap b/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test.snap old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config old mode 100755 new mode 100644 diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml b/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml deleted file mode 100755 index ac8523c..0000000 --- a/subworkflows/nf-core/utils_nfcore_pipeline/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -subworkflows/utils_nfcore_pipeline: - - subworkflows/nf-core/utils_nfcore_pipeline/** diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config index 09ef842..443e828 100644 --- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config +++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow.config @@ -5,4 +5,4 @@ plugins { validation { parametersSchema = "${projectDir}/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json" monochromeLogs = true -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json old mode 100755 new mode 100644 From 44543dff9d9de2811c17d010b781d848d626d089 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Wed, 27 Aug 2025 15:02:04 +0200 Subject: [PATCH 03/27] update stub pipeline test --- tests/preprocess_stub.nf.test | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/preprocess_stub.nf.test b/tests/preprocess_stub.nf.test index bbb0747..8dbab90 100644 --- a/tests/preprocess_stub.nf.test +++ b/tests/preprocess_stub.nf.test @@ -3,6 +3,7 @@ nextflow_pipeline { name "Test preprocess workflow stub" script "../main.nf" tag "stub" + profile "docker" test("-profile test, stub") { options "-stub" From 48e6e390a18e50c668174f4f53324841c4cd0937 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Wed, 27 Aug 2025 16:02:06 +0200 Subject: [PATCH 04/27] update snapshots pipeline level tests, update config files --- nf-test.config | 2 +- tests/default.nf.test.snap | 72 +++++++++++++++--------------- tests/preprocess.nf.test | 2 +- tests/preprocess.nf.test.snap | 6 +-- tests/preprocess_stub.nf.test | 3 +- tests/preprocess_stub.nf.test.snap | 4 +- 6 files changed, 45 insertions(+), 44 deletions(-) diff --git a/nf-test.config b/nf-test.config index 2285cf7..604f3b6 100644 --- a/nf-test.config +++ b/nf-test.config @@ -12,7 +12,7 @@ config { ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*' // run all test with defined profile(s) from the main nextflow.config - profile "docker" + profile "test, docker" // list of filenames or patterns that should be trigger a full test run triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore' diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index cc440cd..dd39d96 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -309,50 +309,50 @@ "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.mat:md5,d4fd21cb383f0d0df184e465a32dc371", + "NM_variables.mat:md5,e706418c4724b2a400365dff7a6af338", "TEST1_ctip2_full.tif:md5,fb17be9f66140c674dad1c0eba3b7a2e", "TEST1_topro_full.tif:md5,5e6784fc7062215bc6538ccccc49a5f4", - "alignment_table.mat:md5,dc6aa795b35001c33f6ff0d452fa0140", - "path_table.mat:md5,f5f0e887c50b838e69efda046047609c", - "z_displacement_align.mat:md5,514f304bf6633cc2eeba8849f15fa9c6", - "NM_variables.mat:md5,25ed9a52821de96068683ba5d4454967", + "alignment_table.mat:md5,d7a13d06d9e5e7066f4b512164a18f2a", + "path_table.mat:md5,6252baaa86f0aa1bf7ed81766ee7febd", + "z_displacement_align.mat:md5,7fd164065274fadbed2fcea788985b82", + "NM_variables.mat:md5,4d55500a124c677a44465ebc346c4412", "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,f67ff3bff41158505ac1132e542d8bd6", - "flatfield_2.png:md5,5c915f810b286aa1853898618319ee3a", - "tile_adj_1.png:md5,3f84630dbfe72af950516239a5838f87", - "tile_adj_2.png:md5,0c96ca9bbafdfd47ab413d7fc17d3bb9", + "flatfield_1.png:md5,70d9797c9cf2c02eaad4cb86f329b394", + "flatfield_2.png:md5,71db816055e579cdba42eb05d643613e", + "tile_adj_1.png:md5,195ac96ac1ea0e05a3ca41d662f9e752", + "tile_adj_2.png:md5,2b4431096c0d8fd1f4c4e9ad7da1b7f6", "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:md5,3a85c52f8668f056a442eaa713b85a8a", - "y_adj_2.png:md5,89e23f87bd9e0a05b5730bb566cd134f", - "adj_params.mat:md5,90c091ead6ba2cba4e48f24587b45f70", - "path_table.mat:md5,9564bdf930d56079e3991e2b6fb57a99", - "thresholds.mat:md5,5882bf41afd5ffa7060070dd247d8979", - "NM_variables.json:md5,5cd546cfb4f252cfdba288c58bda09e7", - "alignment_table.json:md5,d8aa800041cb30a175141e7bae84e450", - "path_table.json:md5,c1794aeb366490cfdc47315f58c559d0", + "y_adj_1.png:md5,be0b43fbbab1c720fb3217c87c8efc6a", + "y_adj_2.png:md5,e4595f36fcd0d0ef18ae57a976a736cb", + "adj_params.mat:md5,0900ce9bf36aee491587d1b903e85565", + "path_table.mat:md5,376cb8ff82de242309c51142ab096680", + "thresholds.mat:md5,bbda95aded722f6ec39dc500891e97e9", + "NM_variables.json:md5,973db6a0c69f126cb3d8bdbff898d961", + "alignment_table.json:md5,05b6f7bf8fbb43d553c438c7de933b7c", + "path_table.json:md5,9f5563e822b2a231d0cc2709ee193f6e", "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", - "NM_variables.json:md5,5cd546cfb4f252cfdba288c58bda09e7", - "adj_params.json:md5,b3951bdfa4d7f6539633c636ee2d06f0", - "path_table.json:md5,c1794aeb366490cfdc47315f58c559d0", - "thresholds.json:md5,39f24ba432b56e133aa9ff75fd35e79f", - "adj_params.json:md5,b3951bdfa4d7f6539633c636ee2d06f0", - "adjusted_z.csv:md5,363f2ef6c65a276bddd84b3939e240bd", - "alignment_table.json:md5,d8aa800041cb30a175141e7bae84e450", - "path_table.json:md5,c1794aeb366490cfdc47315f58c559d0", + "NM_variables.json:md5,973db6a0c69f126cb3d8bdbff898d961", + "adj_params.json:md5,05ccfd257b06a2a825abffd5680fa4e4", + "path_table.json:md5,9f5563e822b2a231d0cc2709ee193f6e", + "thresholds.json:md5,dd08458146588268db81b66d699236f4", + "adj_params.json:md5,05ccfd257b06a2a825abffd5680fa4e4", + "adjusted_z.csv:md5,d7b98b45ad6b3ac13cff31aa13ca8107", + "alignment_table.json:md5,05b6f7bf8fbb43d553c438c7de933b7c", + "path_table.json:md5,9f5563e822b2a231d0cc2709ee193f6e", "stitch_tforms.json:md5,b5cc9b439f94631bee62e3f8315dd9aa", - "thresholds.json:md5,39f24ba432b56e133aa9ff75fd35e79f", + "thresholds.json:md5,dd08458146588268db81b66d699236f4", "z_disp_matrix.json:md5,575020a27eee808b03c615e0a80ca506", "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", "versions.yml:md5,2525ed35a50c7d43e50daf45c81e2502", "TEST1.csv:md5,03ade2aa5a38d978f6b1dd34d741844a", "TEST1_counts.csv:md5,466295dc5cb794e773520be014ee38ee", - "NM_variables.mat:md5,0fe75932ca748a69c8f1dc1457ffd172", + "NM_variables.mat:md5,9606c399e1960c0d5a0412c2a96d0051", "TEST1_0001_C1_topro_stitched.tif:md5,317719086b501e2ff598b6378b5000bc", "TEST1_0001_C2_ctip2_stitched.tif:md5,1425cb6fb2329192c34dabc4cdeb608b", "TEST1_0002_C1_topro_stitched.tif:md5,acd2b0c07253e62a51a2211835ee8af3", @@ -389,14 +389,14 @@ "TEST1_0017_C2_ctip2_stitched.tif:md5,fb252141f1e9c3344c44acb97bf6b9f6", "TEST1_0018_C1_topro_stitched.tif:md5,685c86092c751a15c7bc692af8ea9202", "TEST1_0018_C2_ctip2_stitched.tif:md5,2c559e7593d692e1b399a9de4f83e250", - "adj_params.mat:md5,90c091ead6ba2cba4e48f24587b45f70", - "adjusted_z.mat:md5,a419aa5fc27b146391acc57ce17abd09", - "alignment_table.mat:md5,dc6aa795b35001c33f6ff0d452fa0140", - "path_table.mat:md5,f5f0e887c50b838e69efda046047609c", - "stitch_tforms.mat:md5,3375a5903faa1c43d475368b7514f7fb", - "thresholds.mat:md5,5882bf41afd5ffa7060070dd247d8979", - "z_disp_matrix.mat:md5,bd0e6b256650d504d95b00083cfdc459", - "z_displacement_align.mat:md5,514f304bf6633cc2eeba8849f15fa9c6", + "adj_params.mat:md5,0900ce9bf36aee491587d1b903e85565", + "adjusted_z.mat:md5,14ee5325f681609396aee2c92bad3603", + "alignment_table.mat:md5,d7a13d06d9e5e7066f4b512164a18f2a", + "path_table.mat:md5,6252baaa86f0aa1bf7ed81766ee7febd", + "stitch_tforms.mat:md5,f627a1e3d70258a0b0299b81f47ac226", + "thresholds.mat:md5,bbda95aded722f6ec39dc500891e97e9", + "z_disp_matrix.mat:md5,73aa0678963e363a8807945f2571a416", + "z_displacement_align.mat:md5,7fd164065274fadbed2fcea788985b82", "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", @@ -571,6 +571,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-27T12:44:17.082585224" + "timestamp": "2025-08-27T16:00:17.700403194" } } \ No newline at end of file diff --git a/tests/preprocess.nf.test b/tests/preprocess.nf.test index 533fada..db312fc 100644 --- a/tests/preprocess.nf.test +++ b/tests/preprocess.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "cpu" tag "pipeline_lsmquant" - profile "test" + test("-profile test preprocess") { diff --git a/tests/preprocess.nf.test.snap b/tests/preprocess.nf.test.snap index 5ba06fd..624b99d 100644 --- a/tests/preprocess.nf.test.snap +++ b/tests/preprocess.nf.test.snap @@ -1,5 +1,5 @@ { - "-profile test": { + "-profile test preprocess": { "content": [ 7, { @@ -305,8 +305,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-17T10:34:04.048462839" + "timestamp": "2025-08-27T15:18:36.331336339" } } \ No newline at end of file diff --git a/tests/preprocess_stub.nf.test b/tests/preprocess_stub.nf.test index 8dbab90..dba49e4 100644 --- a/tests/preprocess_stub.nf.test +++ b/tests/preprocess_stub.nf.test @@ -3,7 +3,8 @@ nextflow_pipeline { name "Test preprocess workflow stub" script "../main.nf" tag "stub" - profile "docker" + + test("-profile test, stub") { options "-stub" diff --git a/tests/preprocess_stub.nf.test.snap b/tests/preprocess_stub.nf.test.snap index ae53eff..e62ae3d 100644 --- a/tests/preprocess_stub.nf.test.snap +++ b/tests/preprocess_stub.nf.test.snap @@ -70,8 +70,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-18T16:24:14.749062629" + "timestamp": "2025-08-27T15:05:48.419447313" } } \ No newline at end of file From bb0c6504862459533813a8b7d3ed24b2ce6f4906 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 28 Aug 2025 18:53:15 +0200 Subject: [PATCH 05/27] update pipeline level test + snapshot --- conf/modules.config | 114 ++------- tests/.nftignore | 9 + tests/default.nf.test | 2 +- tests/default.nf.test.snap | 271 ++++++++++----------- tests/preprocess.nf.test | 6 +- tests/preprocess.nf.test.snap | 434 +++++++++++++++++++++++++--------- 6 files changed, 482 insertions(+), 354 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 905140c..c62eb64 100755 --- a/conf/modules.config +++ b/conf/modules.config @@ -30,164 +30,91 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] } - + /* withName: 'MAT2JSON' { publishDir = [ path: { "${params.outdir}/${meta.id}/mat2json" }, mode: params.publish_dir_mode ] } + */ + withName: 'NUMORPHINTENSITY' { publishDir = [ - path: { "${params.outdir}/${meta.id}/intensity/samples" }, - mode: params.publish_dir_mode, - pattern: 'results/samples/intensity_adjustment/*', - saveAs: { filename -> - if (filename.equals('versions.yml')) { - null - } else { - filename.replaceFirst('^results/samples/intensity_adjustment/', 'samples/intensity_adjustment/') - } - } - ] - publishDir = [ - path: { "${params.outdir}/${meta.id}/intensity/variables" }, + path: { "${params.outdir}/numorphintensity/" }, mode: params.publish_dir_mode, - pattern: 'results/variables/*', + pattern: 'results/**/*', saveAs: { filename -> if (filename.equals('versions.yml')) { null } else { - filename.replaceFirst('^results/variables/', 'variables/') + filename.replaceFirst("^results/", "${meta.id}/") } } ] - publishDir = [ - path: { "${params.outdir}/${meta.id}/intensity/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - - ] - } withName: 'NUMORPHALIGN' { publishDir = [ - path: { "${params.outdir}/${meta.id}/alignment/samples" }, + path: { "${params.outdir}/numorphalign/" }, mode: params.publish_dir_mode, - pattern: 'results/samples/alignment/*', + pattern: 'results/**/*', saveAs: { filename -> if (filename.equals('versions.yml')) { null } else { - filename.replaceFirst('^results/samples/alignment/', 'samples/alignment/') + filename.replaceFirst("^results/", "${meta.id}/") } } ] - publishDir = [ - path: { "${params.outdir}/${meta.id}/alignment/variables" }, - mode: params.publish_dir_mode, - pattern: 'results/variables/*', - saveAs: { filename -> - if (filename.equals('versions.yml')) { - null - } else { - filename.replaceFirst('^results/variables/', 'variables/') - } - } - ] - publishDir = [ - path: { "${params.outdir}/${meta.id}/alignment/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: 'NUMORPHSTITCH' { publishDir = [ - path: { "${params.outdir}/${meta.id}/stitching/variables" }, + path: { "${params.outdir}/numorphstitch/" }, mode: params.publish_dir_mode, - pattern: 'results/variables/*', + pattern: 'results/**/*', saveAs: { filename -> if (filename.equals('versions.yml')) { null } else { - filename.replaceFirst('^results/variables/', 'variables/') + filename.replaceFirst("^results/", "${meta.id}/") } } ] - publishDir = [ - path: { "${params.outdir}/${meta.id}/stitching/stitched" }, - mode: params.publish_dir_mode, - pattern: 'results/stitched/*', - saveAs: { filename -> - if (filename.equals('versions.yml')) { - null - } else { - filename.replaceFirst('^results/stitched/', 'stitched/') - } - } - ] - publishDir = [ - path: { "${params.outdir}/${meta.id}/stitching/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: 'NUMORPHRESAMPLE' { publishDir = [ - path: { "${params.outdir}/${meta.id}/resampling/resampled/" }, + path: { "${params.outdir}/numorphresample/" }, mode: params.publish_dir_mode, - pattern: 'results/resampled/*', + pattern: 'results/**/*', saveAs: { filename -> if (filename.equals('versions.yml')) { null } else { - filename.replaceFirst('^results/resampled/', 'resampled/') + filename.replaceFirst("^results/", "${meta.id}/") } } ] - publishDir = [ - path: { "${params.outdir}/${meta.id}/resampling/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: 'NUMORPHREGISTER' { publishDir = [ - path: { "${params.outdir}/${meta.id}/register/registered/" }, + path: { "${params.outdir}/numorphregister/" }, mode: params.publish_dir_mode, - pattern: 'results/registered/*', + pattern: 'results/**/*', saveAs: { filename -> if (filename.equals('versions.yml')) { null } else { - filename.replaceFirst('^results/registered/', 'registered/') + filename.replaceFirst("^results/", "${meta.id}/") } } ] - publishDir = [ - path: { "${params.outdir}/${meta.id}/register/variables" }, - mode: params.publish_dir_mode, - pattern: 'results/variables/*', - saveAs: { filename -> - if (filename.equals('versions.yml')) { - null - } else { - filename.replaceFirst('^results/variables/', 'variables/') - } - } - ] - publishDir = [ - path: { "${params.outdir}/${meta.id}/register/" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] } withName: 'NUMORPH3DUNET' { publishDir = [ - path: { "${params.outdir}/${meta.id}/segmentation/" }, + path: { "${params.outdir}/numorph3dunet/" }, mode: params.publish_dir_mode, pattern: 'results/*', saveAs: { filename -> @@ -195,9 +122,10 @@ process { null } else { - filename.replaceFirst('^results/', '') + filename.replaceFirst("^results/", "${meta.id}/") } } ] } + } diff --git a/tests/.nftignore b/tests/.nftignore index 158c83c..3ebeb10 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -9,3 +9,12 @@ multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html fastqc/*_fastqc.{html,zip} pipeline_info/*.{html,json,txt,yml} +{numorphintensity,numorphalign,numorphstitch,numorphregister,numorphresample}/*/NM_variables.mat +{numorphintensity,numorphalign,numorphstitch}/*/*/path_table.mat +numorphalign/*/*/alignment_table.mat +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 diff --git a/tests/default.nf.test b/tests/default.nf.test index 13668ea..a3b22b9 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -6,7 +6,7 @@ nextflow_pipeline { tag "gpu" profile "docker,test_gpu" - test("-profile test_gpu") { + test("default test gpu") { when { params { diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index dd39d96..1607fb1 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,5 +1,5 @@ { - "-profile test_gpu": { + "default test gpu": { "content": [ 8, { @@ -26,114 +26,110 @@ } }, [ - "TEST1", - "TEST1/alignment", - "TEST1/alignment/results", - "TEST1/alignment/results/NM_variables.mat", - "TEST1/alignment/results/samples", - "TEST1/alignment/results/samples/alignment", - "TEST1/alignment/results/samples/alignment/TEST1_ctip2_full.tif", - "TEST1/alignment/results/samples/alignment/TEST1_topro_full.tif", - "TEST1/alignment/results/variables", - "TEST1/alignment/results/variables/alignment_table.mat", - "TEST1/alignment/results/variables/path_table.mat", - "TEST1/alignment/results/variables/z_displacement_align.mat", - "TEST1/intensity", - "TEST1/intensity/results", - "TEST1/intensity/results/NM_variables.mat", - "TEST1/intensity/results/samples", - "TEST1/intensity/results/samples/intensity_adjustment", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/flatfield_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/flatfield_2.png", - "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_2.png", - "TEST1/intensity/results/samples/intensity_adjustment/topro_1_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_1_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_2_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_2_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/y_adj_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/y_adj_2.png", - "TEST1/intensity/results/variables", - "TEST1/intensity/results/variables/adj_params.mat", - "TEST1/intensity/results/variables/path_table.mat", - "TEST1/intensity/results/variables/thresholds.mat", - "TEST1/mat2json", - "TEST1/mat2json/align", - "TEST1/mat2json/align/NM_variables.json", - "TEST1/mat2json/align/alignment_table.json", - "TEST1/mat2json/align/path_table.json", - "TEST1/mat2json/align/z_displacement_align.json", - "TEST1/mat2json/intensity", - "TEST1/mat2json/intensity/NM_variables.json", - "TEST1/mat2json/intensity/adj_params.json", - "TEST1/mat2json/intensity/path_table.json", - "TEST1/mat2json/intensity/thresholds.json", - "TEST1/mat2json/stitch", - "TEST1/mat2json/stitch/adj_params.json", - "TEST1/mat2json/stitch/adjusted_z.csv", - "TEST1/mat2json/stitch/alignment_table.json", - "TEST1/mat2json/stitch/path_table.json", - "TEST1/mat2json/stitch/stitch_tforms.json", - "TEST1/mat2json/stitch/thresholds.json", - "TEST1/mat2json/stitch/z_disp_matrix.json", - "TEST1/mat2json/stitch/z_displacement_align.json", - "TEST1/mat2json/versions.yml", - "TEST1/segmentation", - "TEST1/segmentation/TEST1.csv", - "TEST1/segmentation/TEST1_counts.csv", - "TEST1/stitching", - "TEST1/stitching/results", - "TEST1/stitching/results/NM_variables.mat", - "TEST1/stitching/results/stitched", - "TEST1/stitching/results/stitched/TEST1_0001_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0001_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0002_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0002_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0003_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0003_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0004_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0004_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0005_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0005_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0006_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0006_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0007_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0007_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0008_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0008_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0009_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0009_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0010_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0010_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0011_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0011_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0012_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0012_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0013_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0013_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0014_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0014_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0015_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0015_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0016_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0016_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0017_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0017_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0018_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0018_C2_ctip2_stitched.tif", - "TEST1/stitching/results/variables", - "TEST1/stitching/results/variables/adj_params.mat", - "TEST1/stitching/results/variables/adjusted_z.mat", - "TEST1/stitching/results/variables/alignment_table.mat", - "TEST1/stitching/results/variables/path_table.mat", - "TEST1/stitching/results/variables/stitch_tforms.mat", - "TEST1/stitching/results/variables/thresholds.mat", - "TEST1/stitching/results/variables/z_disp_matrix.mat", - "TEST1/stitching/results/variables/z_displacement_align.mat", + "mat2json", + "mat2json/align", + "mat2json/align/NM_variables.json", + "mat2json/align/alignment_table.json", + "mat2json/align/path_table.json", + "mat2json/align/z_displacement_align.json", + "mat2json/intensity", + "mat2json/intensity/NM_variables.json", + "mat2json/intensity/adj_params.json", + "mat2json/intensity/path_table.json", + "mat2json/intensity/thresholds.json", + "mat2json/stitch", + "mat2json/stitch/adj_params.json", + "mat2json/stitch/adjusted_z.csv", + "mat2json/stitch/alignment_table.json", + "mat2json/stitch/path_table.json", + "mat2json/stitch/stitch_tforms.json", + "mat2json/stitch/thresholds.json", + "mat2json/stitch/z_disp_matrix.json", + "mat2json/stitch/z_displacement_align.json", + "numorph3dunet", + "numorph3dunet/TEST1", + "numorph3dunet/TEST1/TEST1.csv", + "numorph3dunet/TEST1/TEST1_counts.csv", + "numorphalign", + "numorphalign/TEST1", + "numorphalign/TEST1/samples", + "numorphalign/TEST1/samples/alignment", + "numorphalign/TEST1/samples/alignment/TEST1_ctip2_full.tif", + "numorphalign/TEST1/samples/alignment/TEST1_topro_full.tif", + "numorphalign/TEST1/variables", + "numorphalign/TEST1/variables/alignment_table.mat", + "numorphalign/TEST1/variables/path_table.mat", + "numorphalign/TEST1/variables/z_displacement_align.mat", + "numorphintensity", + "numorphintensity/TEST1", + "numorphintensity/TEST1/samples", + "numorphintensity/TEST1/samples/intensity_adjustment", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_2.png", + "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_2.png", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_2.png", + "numorphintensity/TEST1/variables", + "numorphintensity/TEST1/variables/adj_params.mat", + "numorphintensity/TEST1/variables/path_table.mat", + "numorphintensity/TEST1/variables/thresholds.mat", + "numorphstitch", + "numorphstitch/TEST1", + "numorphstitch/TEST1/stitched", + "numorphstitch/TEST1/stitched/TEST1_0001_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0001_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0002_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0002_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0003_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0003_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0004_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0004_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0005_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0005_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0006_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0006_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0007_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0007_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0008_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0008_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0009_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0009_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0010_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0010_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0011_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0011_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0012_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0012_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0013_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0013_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0014_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0014_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0015_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0015_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0016_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0016_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0017_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0017_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0018_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0018_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/variables", + "numorphstitch/TEST1/variables/adj_params.mat", + "numorphstitch/TEST1/variables/adjusted_z.mat", + "numorphstitch/TEST1/variables/alignment_table.mat", + "numorphstitch/TEST1/variables/path_table.mat", + "numorphstitch/TEST1/variables/stitch_tforms.mat", + "numorphstitch/TEST1/variables/thresholds.mat", + "numorphstitch/TEST1/variables/z_disp_matrix.mat", + "numorphstitch/TEST1/variables/z_displacement_align.mat", "pipeline_info", "pipeline_info/nf_core_lsmquant_software_mqc_versions.yml", "unzip", @@ -309,50 +305,29 @@ "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.mat:md5,e706418c4724b2a400365dff7a6af338", + "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", + "stitch_tforms.json:md5,b5cc9b439f94631bee62e3f8315dd9aa", + "z_disp_matrix.json:md5,575020a27eee808b03c615e0a80ca506", + "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", + "TEST1.csv:md5,03ade2aa5a38d978f6b1dd34d741844a", + "TEST1_counts.csv:md5,466295dc5cb794e773520be014ee38ee", "TEST1_ctip2_full.tif:md5,fb17be9f66140c674dad1c0eba3b7a2e", "TEST1_topro_full.tif:md5,5e6784fc7062215bc6538ccccc49a5f4", - "alignment_table.mat:md5,d7a13d06d9e5e7066f4b512164a18f2a", - "path_table.mat:md5,6252baaa86f0aa1bf7ed81766ee7febd", - "z_displacement_align.mat:md5,7fd164065274fadbed2fcea788985b82", - "NM_variables.mat:md5,4d55500a124c677a44465ebc346c4412", + "z_displacement_align.mat:md5,39474b8b4f1f246e06f8fb0939989141", "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:md5,70d9797c9cf2c02eaad4cb86f329b394", - "flatfield_2.png:md5,71db816055e579cdba42eb05d643613e", - "tile_adj_1.png:md5,195ac96ac1ea0e05a3ca41d662f9e752", - "tile_adj_2.png:md5,2b4431096c0d8fd1f4c4e9ad7da1b7f6", + "flatfield_1.png:md5,d7bb0f7029a40b5a01836a1d76fcc4fe", + "flatfield_2.png:md5,aefc71f6dfef5a51abcfae55547a38b7", + "tile_adj_1.png:md5,2fb1fde009afe7d387d18af329cb5bc8", + "tile_adj_2.png:md5,e7aca3a27fd8df54327192d75e090ed6", "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,be0b43fbbab1c720fb3217c87c8efc6a", - "y_adj_2.png:md5,e4595f36fcd0d0ef18ae57a976a736cb", - "adj_params.mat:md5,0900ce9bf36aee491587d1b903e85565", - "path_table.mat:md5,376cb8ff82de242309c51142ab096680", - "thresholds.mat:md5,bbda95aded722f6ec39dc500891e97e9", - "NM_variables.json:md5,973db6a0c69f126cb3d8bdbff898d961", - "alignment_table.json:md5,05b6f7bf8fbb43d553c438c7de933b7c", - "path_table.json:md5,9f5563e822b2a231d0cc2709ee193f6e", - "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", - "NM_variables.json:md5,973db6a0c69f126cb3d8bdbff898d961", - "adj_params.json:md5,05ccfd257b06a2a825abffd5680fa4e4", - "path_table.json:md5,9f5563e822b2a231d0cc2709ee193f6e", - "thresholds.json:md5,dd08458146588268db81b66d699236f4", - "adj_params.json:md5,05ccfd257b06a2a825abffd5680fa4e4", - "adjusted_z.csv:md5,d7b98b45ad6b3ac13cff31aa13ca8107", - "alignment_table.json:md5,05b6f7bf8fbb43d553c438c7de933b7c", - "path_table.json:md5,9f5563e822b2a231d0cc2709ee193f6e", - "stitch_tforms.json:md5,b5cc9b439f94631bee62e3f8315dd9aa", - "thresholds.json:md5,dd08458146588268db81b66d699236f4", - "z_disp_matrix.json:md5,575020a27eee808b03c615e0a80ca506", - "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", - "versions.yml:md5,2525ed35a50c7d43e50daf45c81e2502", - "TEST1.csv:md5,03ade2aa5a38d978f6b1dd34d741844a", - "TEST1_counts.csv:md5,466295dc5cb794e773520be014ee38ee", - "NM_variables.mat:md5,9606c399e1960c0d5a0412c2a96d0051", + "y_adj_1.png:md5,4658273b8bd4cd6f8ed8ef86c8b16cf7", + "y_adj_2.png:md5,3426316c88c10efc987d14df902218a8", "TEST1_0001_C1_topro_stitched.tif:md5,317719086b501e2ff598b6378b5000bc", "TEST1_0001_C2_ctip2_stitched.tif:md5,1425cb6fb2329192c34dabc4cdeb608b", "TEST1_0002_C1_topro_stitched.tif:md5,acd2b0c07253e62a51a2211835ee8af3", @@ -389,14 +364,6 @@ "TEST1_0017_C2_ctip2_stitched.tif:md5,fb252141f1e9c3344c44acb97bf6b9f6", "TEST1_0018_C1_topro_stitched.tif:md5,685c86092c751a15c7bc692af8ea9202", "TEST1_0018_C2_ctip2_stitched.tif:md5,2c559e7593d692e1b399a9de4f83e250", - "adj_params.mat:md5,0900ce9bf36aee491587d1b903e85565", - "adjusted_z.mat:md5,14ee5325f681609396aee2c92bad3603", - "alignment_table.mat:md5,d7a13d06d9e5e7066f4b512164a18f2a", - "path_table.mat:md5,6252baaa86f0aa1bf7ed81766ee7febd", - "stitch_tforms.mat:md5,f627a1e3d70258a0b0299b81f47ac226", - "thresholds.mat:md5,bbda95aded722f6ec39dc500891e97e9", - "z_disp_matrix.mat:md5,73aa0678963e363a8807945f2571a416", - "z_displacement_align.mat:md5,7fd164065274fadbed2fcea788985b82", "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", @@ -571,6 +538,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-27T16:00:17.700403194" + "timestamp": "2025-08-28T18:17:22.248739072" } } \ No newline at end of file diff --git a/tests/preprocess.nf.test b/tests/preprocess.nf.test index db312fc..51d6810 100644 --- a/tests/preprocess.nf.test +++ b/tests/preprocess.nf.test @@ -17,7 +17,7 @@ nextflow_pipeline { then { def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - def json_files = getAllFilesFromDir(params.outdir, include: ['**/*.json']) + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assert workflow.success assertAll( { assert snapshot( @@ -25,7 +25,9 @@ nextflow_pipeline { workflow.trace.succeeded().size(), removeNextflowVersion("$outputDir/pipeline_info/nf_core_lsmquant_software_mqc_versions.yml"), // All stable path name, with a relative path - stable_name.isEmpty() ? 'No stable paths' : stable_name + stable_name.isEmpty() ? 'No stable paths' : stable_name, + // All files with stable contents + stable_path ).match()} ) } diff --git a/tests/preprocess.nf.test.snap b/tests/preprocess.nf.test.snap index 624b99d..30bbfb2 100644 --- a/tests/preprocess.nf.test.snap +++ b/tests/preprocess.nf.test.snap @@ -23,111 +23,106 @@ } }, [ - "TEST1", - "TEST1/alignment", - "TEST1/alignment/results", - "TEST1/alignment/results/NM_variables.mat", - "TEST1/alignment/results/samples", - "TEST1/alignment/results/samples/alignment", - "TEST1/alignment/results/samples/alignment/TEST1_ctip2_full.tif", - "TEST1/alignment/results/samples/alignment/TEST1_topro_full.tif", - "TEST1/alignment/results/variables", - "TEST1/alignment/results/variables/alignment_table.mat", - "TEST1/alignment/results/variables/path_table.mat", - "TEST1/alignment/results/variables/z_displacement_align.mat", - "TEST1/intensity", - "TEST1/intensity/results", - "TEST1/intensity/results/NM_variables.mat", - "TEST1/intensity/results/samples", - "TEST1/intensity/results/samples/intensity_adjustment", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/flatfield_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/flatfield_2.png", - "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_2.png", - "TEST1/intensity/results/samples/intensity_adjustment/topro_1_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_1_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_2_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_2_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/y_adj_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/y_adj_2.png", - "TEST1/intensity/results/variables", - "TEST1/intensity/results/variables/adj_params.mat", - "TEST1/intensity/results/variables/path_table.mat", - "TEST1/intensity/results/variables/thresholds.mat", - "TEST1/mat2json", - "TEST1/mat2json/align", - "TEST1/mat2json/align/NM_variables.json", - "TEST1/mat2json/align/alignment_table.json", - "TEST1/mat2json/align/path_table.json", - "TEST1/mat2json/align/z_displacement_align.json", - "TEST1/mat2json/intensity", - "TEST1/mat2json/intensity/NM_variables.json", - "TEST1/mat2json/intensity/adj_params.json", - "TEST1/mat2json/intensity/path_table.json", - "TEST1/mat2json/intensity/thresholds.json", - "TEST1/mat2json/stitch", - "TEST1/mat2json/stitch/adj_params.json", - "TEST1/mat2json/stitch/adjusted_z.csv", - "TEST1/mat2json/stitch/alignment_table.json", - "TEST1/mat2json/stitch/path_table.json", - "TEST1/mat2json/stitch/stitch_tforms.json", - "TEST1/mat2json/stitch/thresholds.json", - "TEST1/mat2json/stitch/z_disp_matrix.json", - "TEST1/mat2json/stitch/z_displacement_align.json", - "TEST1/mat2json/versions.yml", - "TEST1/stitching", - "TEST1/stitching/results", - "TEST1/stitching/results/NM_variables.mat", - "TEST1/stitching/results/stitched", - "TEST1/stitching/results/stitched/TEST1_0001_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0001_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0002_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0002_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0003_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0003_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0004_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0004_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0005_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0005_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0006_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0006_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0007_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0007_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0008_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0008_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0009_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0009_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0010_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0010_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0011_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0011_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0012_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0012_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0013_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0013_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0014_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0014_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0015_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0015_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0016_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0016_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0017_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0017_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0018_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0018_C2_ctip2_stitched.tif", - "TEST1/stitching/results/variables", - 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"mat2json/stitch/path_table.json", + "mat2json/stitch/stitch_tforms.json", + "mat2json/stitch/thresholds.json", + "mat2json/stitch/z_disp_matrix.json", + "mat2json/stitch/z_displacement_align.json", + "numorphalign", + "numorphalign/TEST1", + "numorphalign/TEST1/samples", + "numorphalign/TEST1/samples/alignment", + "numorphalign/TEST1/samples/alignment/TEST1_ctip2_full.tif", + "numorphalign/TEST1/samples/alignment/TEST1_topro_full.tif", + "numorphalign/TEST1/variables", + "numorphalign/TEST1/variables/alignment_table.mat", + "numorphalign/TEST1/variables/path_table.mat", + "numorphalign/TEST1/variables/z_displacement_align.mat", + "numorphintensity", + "numorphintensity/TEST1", + "numorphintensity/TEST1/samples", + "numorphintensity/TEST1/samples/intensity_adjustment", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_2_11.tif", + 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Z0619.ome.tif:md5,43d0386b21d9f6a36c209dc3ab60d1cc", + "16-35-34_WT7R_ctip2_topro_2-5x_0-085NA_4z_UltraII[03 x 03]_C01_xyz-Table Z0620.ome.tif:md5,b4f4be8e38b3b84dcd1a34a2b1968abc" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-27T15:18:36.331336339" + "timestamp": "2025-08-28T18:27:59.276965009" } } \ No newline at end of file From 500cea62ca86a6a671fae46524a191fdd1f32875 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Fri, 29 Aug 2025 10:05:12 +0200 Subject: [PATCH 06/27] update preprocess snapshots --- tests/preprocess.nf.test.snap | 16 +++---- tests/preprocess_stub.nf.test.snap | 75 ++++++++++++++---------------- 2 files changed, 43 insertions(+), 48 deletions(-) diff --git a/tests/preprocess.nf.test.snap b/tests/preprocess.nf.test.snap index 30bbfb2..5233fb0 100644 --- a/tests/preprocess.nf.test.snap +++ b/tests/preprocess.nf.test.snap @@ -304,21 +304,21 @@ "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", "TEST1_ctip2_full.tif:md5,fb17be9f66140c674dad1c0eba3b7a2e", "TEST1_topro_full.tif:md5,5e6784fc7062215bc6538ccccc49a5f4", - "z_displacement_align.mat:md5,e6dd356a9e816b7a7cd079f375e288b4", + "z_displacement_align.mat:md5,573223719c05fd3f621fadd468c2dabf", "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:md5,348faeddc9719458ec065d6b6a80a078", - "flatfield_2.png:md5,fd5ad0ce73789c95d15441edfda04a85", - "tile_adj_1.png:md5,a478cd213fe7d75b2cbe537c5a61f075", - "tile_adj_2.png:md5,df6c3cfe426da794436246892389a790", + "flatfield_1.png:md5,1499e8d44ef0fa199d3ae0b0dd8602b3", + "flatfield_2.png:md5,3636cd5855c3c1615e7ad579654183c1", + "tile_adj_1.png:md5,e2032bf09712938c7dd0687570e4548d", + "tile_adj_2.png:md5,aa118ac69fbcc84dfa838a3faf8a973d", "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,cb2b7b2efe3cc5c2a5513e1f0272091d", - "y_adj_2.png:md5,68d39a6223fd11fad4164fb5f32f73b4", + "y_adj_1.png:md5,6c88c69d4561d4863f26f48bac12fbb6", + "y_adj_2.png:md5,1abf810ab0704628391503922259f826", "TEST1_0001_C1_topro_stitched.tif:md5,317719086b501e2ff598b6378b5000bc", "TEST1_0001_C2_ctip2_stitched.tif:md5,1425cb6fb2329192c34dabc4cdeb608b", "TEST1_0002_C1_topro_stitched.tif:md5,acd2b0c07253e62a51a2211835ee8af3", @@ -529,6 +529,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-28T18:27:59.276965009" + "timestamp": "2025-08-29T10:04:25.997678386" } } \ No newline at end of file diff --git a/tests/preprocess_stub.nf.test.snap b/tests/preprocess_stub.nf.test.snap index e62ae3d..ac8108f 100644 --- a/tests/preprocess_stub.nf.test.snap +++ b/tests/preprocess_stub.nf.test.snap @@ -23,45 +23,40 @@ } }, [ - "TEST1", - "TEST1/alignment", - "TEST1/alignment/results", - "TEST1/alignment/results/NM_variables.mat", - "TEST1/alignment/results/samples", - "TEST1/alignment/results/samples/alignment", - "TEST1/alignment/results/samples/alignment/TEST1_full.tif", - "TEST1/alignment/results/variables", - "TEST1/alignment/results/variables/alignment_table.mat", - "TEST1/alignment/results/variables/path_table.mat", - "TEST1/alignment/results/variables/z_displacement_align.mat", - "TEST1/intensity", - "TEST1/intensity/results", - "TEST1/intensity/results/NM_variables.mat", - "TEST1/intensity/results/samples", - "TEST1/intensity/results/samples/intensity_adjustment", - "TEST1/intensity/results/samples/intensity_adjustment/TEST1.png", - "TEST1/intensity/results/variables", - "TEST1/intensity/results/variables/adj_params.mat", - "TEST1/intensity/results/variables/path_table.mat", - "TEST1/intensity/results/variables/thresholds.mat", - "TEST1/mat2json", - "TEST1/mat2json/align", - "TEST1/mat2json/align/TEST1.json", - "TEST1/mat2json/intensity", - "TEST1/mat2json/intensity/TEST1.json", - "TEST1/mat2json/stitch", - "TEST1/mat2json/stitch/TEST1.json", - "TEST1/mat2json/versions.yml", - "TEST1/stitching", - "TEST1/stitching/results", - "TEST1/stitching/results/NM_variables.mat", - "TEST1/stitching/results/stitched", - "TEST1/stitching/results/stitched/TEST1_stitched.tif", - "TEST1/stitching/results/variables", - "TEST1/stitching/results/variables/adjusted_z.mat", - "TEST1/stitching/results/variables/path_table.mat", - "TEST1/stitching/results/variables/stitch_tforms.mat", - "TEST1/stitching/results/variables/z_dips_matrix.mat", + "mat2json", + "mat2json/align", + "mat2json/align/TEST1.json", + "mat2json/intensity", + "mat2json/intensity/TEST1.json", + "mat2json/stitch", + "mat2json/stitch/TEST1.json", + "numorphalign", + "numorphalign/TEST1", + "numorphalign/TEST1/samples", + "numorphalign/TEST1/samples/alignment", + "numorphalign/TEST1/samples/alignment/TEST1_full.tif", + "numorphalign/TEST1/variables", + "numorphalign/TEST1/variables/alignment_table.mat", + "numorphalign/TEST1/variables/path_table.mat", + "numorphalign/TEST1/variables/z_displacement_align.mat", + "numorphintensity", + "numorphintensity/TEST1", + "numorphintensity/TEST1/samples", + "numorphintensity/TEST1/samples/intensity_adjustment", + "numorphintensity/TEST1/samples/intensity_adjustment/TEST1.png", + "numorphintensity/TEST1/variables", + "numorphintensity/TEST1/variables/adj_params.mat", + "numorphintensity/TEST1/variables/path_table.mat", + "numorphintensity/TEST1/variables/thresholds.mat", + "numorphstitch", + "numorphstitch/TEST1", + "numorphstitch/TEST1/stitched", + "numorphstitch/TEST1/stitched/TEST1_stitched.tif", + "numorphstitch/TEST1/variables", + "numorphstitch/TEST1/variables/adjusted_z.mat", + "numorphstitch/TEST1/variables/path_table.mat", + "numorphstitch/TEST1/variables/stitch_tforms.mat", + "numorphstitch/TEST1/variables/z_dips_matrix.mat", "pipeline_info", "pipeline_info/nf_core_lsmquant_software_mqc_versions.yml", "unzip", @@ -72,6 +67,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-27T15:05:48.419447313" + "timestamp": "2025-08-29T09:57:38.849984411" } } \ No newline at end of file From b8ae277cf1fe5db1086d5a05b16de3a616778b80 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Fri, 29 Aug 2025 13:49:24 +0200 Subject: [PATCH 07/27] update all modules and subworkflow tests --- modules/local/mat2json/tests/main.nf.test | 45 +- .../local/mat2json/tests/main.nf.test.snap | 120 ++-- .../numorph3dunet/tests/main.nf.test.snap | 12 +- .../numorphalign/tests/main.nf.test.snap | 71 ++- .../numorphintensity/tests/main.nf.test.snap | 50 +- .../numorphregister/tests/main.nf.test.snap | 8 +- .../numorphstitch/tests/main.nf.test.snap | 223 +++---- .../numorph_preprocessing/tests/.nftignore | 20 + .../numorph_preprocessing/tests/main.nf.test | 42 +- .../tests/main.nf.test.snap | 543 ++++++++++++++++-- 10 files changed, 797 insertions(+), 337 deletions(-) create mode 100644 subworkflows/local/numorph_preprocessing/tests/.nftignore diff --git a/modules/local/mat2json/tests/main.nf.test b/modules/local/mat2json/tests/main.nf.test index af9e03d..2948239 100644 --- a/modules/local/mat2json/tests/main.nf.test +++ b/modules/local/mat2json/tests/main.nf.test @@ -11,21 +11,30 @@ nextflow_process { test("matlab file conversion to json") { when { + params { + outdir = "$workDir" + } process { """ - input[0] = [ - [ id:'test'], // meta map - file('/mnt/ssd/numorph_testdata_s/module_testrun/output_nextflow/intensity/results/variables/thresholds.mat', checkIfExists: true), - ] + input[0] = Channel.fromList([ + tuple([ id:'test'], // meta map + file(params.pipelines_testdata_base_path +'/test_data/mat2json/thresholds.mat', checkIfExists: true)) + ]) + input[1] = Channel.of('test_process') """ } } then { + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + assert workflow.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name.isEmpty() ? 'No stable paths' : stable_name + ).match()} ) } @@ -36,20 +45,30 @@ nextflow_process { options "-stub" when { + params { + outdir = "$workDir" + } process { """ - input[0] = [ - [ id:'test'], // meta map - file('/mnt/ssd/numorph_testdata_s/module_testrun/output_nextflow/intensity/results/variables/thresholds.mat', checkIfExists: true), - ] + input[0] = Channel.fromList([ + tuple([ id:'test'], // meta map + file(params.pipelines_testdata_base_path +'/test_data/mat2json/thresholds.mat', checkIfExists: true)) + ]) + input[1] = Channel.of('test_process') """ } } then { + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + assert workflow.success assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // All stable path name, with a relative path + stable_name.isEmpty() ? 'No stable paths' : stable_name + ).match()} ) } diff --git a/modules/local/mat2json/tests/main.nf.test.snap b/modules/local/mat2json/tests/main.nf.test.snap index ecf9774..e80bf3f 100644 --- a/modules/local/mat2json/tests/main.nf.test.snap +++ b/modules/local/mat2json/tests/main.nf.test.snap @@ -1,80 +1,72 @@ { "matlab file conversion to json": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - [ - "thresholds.json:md5,88adeb36bb657798c80085b6a58ac58b", - "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee" - ] - ] - ], - "1": [ - "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee" - ], - "converted_file": [ - [ - { - "id": "test" - }, - [ - "thresholds.json:md5,88adeb36bb657798c80085b6a58ac58b", - "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee" - ] - ] - ], - "versions": [ - "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee" - ] - } + 1, + [ + "", + "3d", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/.command.begin", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/.command.err", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/.command.log", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/.command.out", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/.command.run", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/.command.sh", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/.command.trace", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/.exitcode", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/test_process", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/test_process/thresholds.json", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/thresholds.mat", + "3d/41b9380a1e0f7ff0bfe8bbc9571e65/versions.yml", + "mat2json", + "mat2json/test_process", + "mat2json/test_process/thresholds.json", + "pipeline_info", + "stage-aeeb1410-b6dd-43cf-8830-583e4cc9920c", + "stage-aeeb1410-b6dd-43cf-8830-583e4cc9920c/e5", + "stage-aeeb1410-b6dd-43cf-8830-583e4cc9920c/e5/ce02fa3d717d9eef7cc5e1c8f28c2b", + "stage-aeeb1410-b6dd-43cf-8830-583e4cc9920c/e5/ce02fa3d717d9eef7cc5e1c8f28c2b/thresholds.mat" + ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-02-21T15:36:22.030027548" + "timestamp": "2025-08-29T13:47:16.889254142" }, "matlab file conversion to json - stub": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - [ - "test.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee" - ] - ] - ], - "1": [ - "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee" - ], - "converted_file": [ - [ - { - "id": "test" - }, - [ - "test.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee" - ] - ] - ], - "versions": [ - "versions.yml:md5,d8fdb19b7f6440f3644b923cf0bf7eee" - ] - } + 1, + [ + "", + "a1", + "a1/d780b4e65514c605e3114f89afd3c3", + "a1/d780b4e65514c605e3114f89afd3c3/.command.begin", + "a1/d780b4e65514c605e3114f89afd3c3/.command.err", + "a1/d780b4e65514c605e3114f89afd3c3/.command.log", + "a1/d780b4e65514c605e3114f89afd3c3/.command.out", + "a1/d780b4e65514c605e3114f89afd3c3/.command.run", + "a1/d780b4e65514c605e3114f89afd3c3/.command.sh", + "a1/d780b4e65514c605e3114f89afd3c3/.command.trace", + "a1/d780b4e65514c605e3114f89afd3c3/.exitcode", + "a1/d780b4e65514c605e3114f89afd3c3/test_process", + "a1/d780b4e65514c605e3114f89afd3c3/test_process/test.json", + "a1/d780b4e65514c605e3114f89afd3c3/thresholds.mat", + "a1/d780b4e65514c605e3114f89afd3c3/versions.yml", + "mat2json", + "mat2json/test_process", + "mat2json/test_process/test.json", + "pipeline_info", + "stage-2314e94b-b9f6-47fa-bd5f-6f79870c5ff9", + "stage-2314e94b-b9f6-47fa-bd5f-6f79870c5ff9/2d", + "stage-2314e94b-b9f6-47fa-bd5f-6f79870c5ff9/2d/4d62c64425c45ecf74be0192f5dc0f", + "stage-2314e94b-b9f6-47fa-bd5f-6f79870c5ff9/2d/4d62c64425c45ecf74be0192f5dc0f/thresholds.mat" + ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-02-21T15:36:26.450520824" + "timestamp": "2025-08-29T13:47:21.509083297" } } \ No newline at end of file diff --git a/modules/local/numorph3dunet/tests/main.nf.test.snap b/modules/local/numorph3dunet/tests/main.nf.test.snap index c6faf83..84ee3c0 100644 --- a/modules/local/numorph3dunet/tests/main.nf.test.snap +++ b/modules/local/numorph3dunet/tests/main.nf.test.snap @@ -3,10 +3,10 @@ "content": [ 2, [ - "TEST1", - "TEST1/segmentation", - "TEST1/segmentation/TEST1.csv", - "TEST1/segmentation/TEST1_counts.csv", + "numorph3dunet", + "numorph3dunet/TEST1", + "numorph3dunet/TEST1/TEST1.csv", + "numorph3dunet/TEST1/TEST1_counts.csv", "pipeline_info", "unzipfiles", "unzipfiles/TEST1", @@ -33,8 +33,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-08-22T14:38:25.745842362" + "timestamp": "2025-08-29T11:55:03.555806608" } } \ No newline at end of file diff --git a/modules/local/numorphalign/tests/main.nf.test.snap b/modules/local/numorphalign/tests/main.nf.test.snap index d55088f..867b952 100644 --- a/modules/local/numorphalign/tests/main.nf.test.snap +++ b/modules/local/numorphalign/tests/main.nf.test.snap @@ -3,41 +3,38 @@ "content": [ 3, [ - "TEST1", - "TEST1/alignment", - "TEST1/alignment/results", - "TEST1/alignment/results/NM_variables.mat", - "TEST1/alignment/results/samples", - "TEST1/alignment/results/samples/alignment", - "TEST1/alignment/results/samples/alignment/TEST1_ctip2_full.tif", - "TEST1/alignment/results/samples/alignment/TEST1_topro_full.tif", - "TEST1/alignment/results/variables", - "TEST1/alignment/results/variables/alignment_table.mat", - "TEST1/alignment/results/variables/path_table.mat", - "TEST1/alignment/results/variables/z_displacement_align.mat", - "TEST1/intensity", - "TEST1/intensity/results", - "TEST1/intensity/results/NM_variables.mat", - "TEST1/intensity/results/samples", - "TEST1/intensity/results/samples/intensity_adjustment", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/flatfield_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/flatfield_2.png", - "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_2.png", - "TEST1/intensity/results/samples/intensity_adjustment/topro_1_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_1_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_2_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_2_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/y_adj_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/y_adj_2.png", - "TEST1/intensity/results/variables", - "TEST1/intensity/results/variables/adj_params.mat", - "TEST1/intensity/results/variables/path_table.mat", - "TEST1/intensity/results/variables/thresholds.mat", + "numorphalign", + "numorphalign/TEST1", + "numorphalign/TEST1/samples", + "numorphalign/TEST1/samples/alignment", + "numorphalign/TEST1/samples/alignment/TEST1_ctip2_full.tif", + "numorphalign/TEST1/samples/alignment/TEST1_topro_full.tif", + "numorphalign/TEST1/variables", + "numorphalign/TEST1/variables/alignment_table.mat", + "numorphalign/TEST1/variables/path_table.mat", + "numorphalign/TEST1/variables/z_displacement_align.mat", + "numorphintensity", + "numorphintensity/TEST1", + "numorphintensity/TEST1/samples", + "numorphintensity/TEST1/samples/intensity_adjustment", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_2.png", + "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_2.png", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_2.png", + "numorphintensity/TEST1/variables", + "numorphintensity/TEST1/variables/adj_params.mat", + "numorphintensity/TEST1/variables/path_table.mat", + "numorphintensity/TEST1/variables/thresholds.mat", "pipeline_info", "unzip", "unzip/TEST1", @@ -214,8 +211,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-20T17:58:04.410259477" + "timestamp": "2025-08-29T11:32:20.483087568" } } \ No newline at end of file diff --git a/modules/local/numorphintensity/tests/main.nf.test.snap b/modules/local/numorphintensity/tests/main.nf.test.snap index 0504bde..7fa6be4 100644 --- a/modules/local/numorphintensity/tests/main.nf.test.snap +++ b/modules/local/numorphintensity/tests/main.nf.test.snap @@ -3,30 +3,28 @@ "content": [ 2, [ - "TEST1", - "TEST1/intensity", - "TEST1/intensity/results", - "TEST1/intensity/results/NM_variables.mat", - "TEST1/intensity/results/samples", - "TEST1/intensity/results/samples/intensity_adjustment", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/flatfield_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/flatfield_2.png", - "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_2.png", - "TEST1/intensity/results/samples/intensity_adjustment/topro_1_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_1_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_2_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_2_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/y_adj_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/y_adj_2.png", - "TEST1/intensity/results/variables", - "TEST1/intensity/results/variables/adj_params.mat", - "TEST1/intensity/results/variables/path_table.mat", - "TEST1/intensity/results/variables/thresholds.mat", + "numorphintensity", + "numorphintensity/TEST1", + "numorphintensity/TEST1/samples", + "numorphintensity/TEST1/samples/intensity_adjustment", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_2.png", + "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_2.png", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_2.png", + "numorphintensity/TEST1/variables", + "numorphintensity/TEST1/variables/adj_params.mat", + "numorphintensity/TEST1/variables/path_table.mat", + "numorphintensity/TEST1/variables/thresholds.mat", "pipeline_info", "unzip", "unzip/TEST1", @@ -203,8 +201,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-20T16:19:48.305625041" + "timestamp": "2025-08-29T11:27:18.418645149" } } \ No newline at end of file diff --git a/modules/local/numorphregister/tests/main.nf.test.snap b/modules/local/numorphregister/tests/main.nf.test.snap index 9e59cad..9581366 100644 --- a/modules/local/numorphregister/tests/main.nf.test.snap +++ b/modules/local/numorphregister/tests/main.nf.test.snap @@ -15,7 +15,7 @@ "TEST1_registered.tif:md5,d41d8cd98f00b204e9800998ecf8427e" ], "4": [ - "versions.yml:md5,8fb479aa14a9e667a80a4e374bd3c302" + "versions.yml:md5,fe89c175cbba844c4b95437e4def7abe" ], "NM_variables": [ "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -30,14 +30,14 @@ "TEST1_registered.tif:md5,d41d8cd98f00b204e9800998ecf8427e" ], "versions": [ - "versions.yml:md5,8fb479aa14a9e667a80a4e374bd3c302" + "versions.yml:md5,fe89c175cbba844c4b95437e4def7abe" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-02-20T15:23:33.270945314" + "timestamp": "2025-08-29T11:37:58.144917362" } } \ No newline at end of file diff --git a/modules/local/numorphstitch/tests/main.nf.test.snap b/modules/local/numorphstitch/tests/main.nf.test.snap index 3a4aef7..ffc64a8 100644 --- a/modules/local/numorphstitch/tests/main.nf.test.snap +++ b/modules/local/numorphstitch/tests/main.nf.test.snap @@ -1,147 +1,88 @@ { - "Numorphstitch stub test": { - "content": [ - { - "0": [ - [ - { - "id": "TEST1" - }, - "TEST1_stitched.tif:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - [ - "adjusted_z.mat:md5,d41d8cd98f00b204e9800998ecf8427e", - "path_table.mat:md5,d41d8cd98f00b204e9800998ecf8427e", - "stitch_tforms.mat:md5,d41d8cd98f00b204e9800998ecf8427e", - "z_dips_matrix.mat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "2": [ - "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "3": [ - "versions.yml:md5,078a96bac91c7c12facb9f321644c34d" - ], - "NM_variables": [ - "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "stitched": [ - [ - { - "id": "TEST1" - }, - "TEST1_stitched.tif:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "variables": [ - [ - "adjusted_z.mat:md5,d41d8cd98f00b204e9800998ecf8427e", - "path_table.mat:md5,d41d8cd98f00b204e9800998ecf8427e", - "stitch_tforms.mat:md5,d41d8cd98f00b204e9800998ecf8427e", - "z_dips_matrix.mat:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,078a96bac91c7c12facb9f321644c34d" - ] - } - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.3" - }, - "timestamp": "2025-02-19T16:40:56.52260208" - }, "Numorphstitch test": { "content": [ 4, [ - "TEST1", - "TEST1/alignment", - "TEST1/alignment/results", - "TEST1/alignment/results/NM_variables.mat", - "TEST1/alignment/results/samples", - "TEST1/alignment/results/samples/alignment", - "TEST1/alignment/results/samples/alignment/TEST1_ctip2_full.tif", - "TEST1/alignment/results/samples/alignment/TEST1_topro_full.tif", - "TEST1/alignment/results/variables", - "TEST1/alignment/results/variables/alignment_table.mat", - "TEST1/alignment/results/variables/path_table.mat", - "TEST1/alignment/results/variables/z_displacement_align.mat", - "TEST1/intensity", - "TEST1/intensity/results", - "TEST1/intensity/results/NM_variables.mat", - "TEST1/intensity/results/samples", - "TEST1/intensity/results/samples/intensity_adjustment", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_1_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/ctip2_2_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/flatfield_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/flatfield_2.png", - "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/tile_adj_2.png", - "TEST1/intensity/results/samples/intensity_adjustment/topro_1_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_1_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_2_1_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/topro_2_2_11.tif", - "TEST1/intensity/results/samples/intensity_adjustment/y_adj_1.png", - "TEST1/intensity/results/samples/intensity_adjustment/y_adj_2.png", - "TEST1/intensity/results/variables", - "TEST1/intensity/results/variables/adj_params.mat", - "TEST1/intensity/results/variables/path_table.mat", - "TEST1/intensity/results/variables/thresholds.mat", - "TEST1/stitching", - "TEST1/stitching/results", - "TEST1/stitching/results/NM_variables.mat", - "TEST1/stitching/results/stitched", - "TEST1/stitching/results/stitched/TEST1_0001_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0001_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0002_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0002_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0003_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0003_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0004_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0004_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0005_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0005_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0006_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0006_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0007_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0007_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0008_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0008_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0009_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0009_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0010_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0010_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0011_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0011_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0012_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0012_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0013_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0013_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0014_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0014_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0015_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0015_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0016_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0016_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0017_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0017_C2_ctip2_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0018_C1_topro_stitched.tif", - "TEST1/stitching/results/stitched/TEST1_0018_C2_ctip2_stitched.tif", - "TEST1/stitching/results/variables", - "TEST1/stitching/results/variables/adj_params.mat", - "TEST1/stitching/results/variables/adjusted_z.mat", - "TEST1/stitching/results/variables/alignment_table.mat", - "TEST1/stitching/results/variables/path_table.mat", - "TEST1/stitching/results/variables/stitch_tforms.mat", - "TEST1/stitching/results/variables/thresholds.mat", - "TEST1/stitching/results/variables/z_disp_matrix.mat", - "TEST1/stitching/results/variables/z_displacement_align.mat", + "numorphalign", + "numorphalign/TEST1", + "numorphalign/TEST1/samples", + "numorphalign/TEST1/samples/alignment", + "numorphalign/TEST1/samples/alignment/TEST1_ctip2_full.tif", + "numorphalign/TEST1/samples/alignment/TEST1_topro_full.tif", + "numorphalign/TEST1/variables", + "numorphalign/TEST1/variables/alignment_table.mat", + "numorphalign/TEST1/variables/path_table.mat", + "numorphalign/TEST1/variables/z_displacement_align.mat", + "numorphintensity", + "numorphintensity/TEST1", + "numorphintensity/TEST1/samples", + "numorphintensity/TEST1/samples/intensity_adjustment", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_2.png", + "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_2.png", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_2.png", + "numorphintensity/TEST1/variables", + "numorphintensity/TEST1/variables/adj_params.mat", + "numorphintensity/TEST1/variables/path_table.mat", + "numorphintensity/TEST1/variables/thresholds.mat", + "numorphstitch", + "numorphstitch/TEST1", + "numorphstitch/TEST1/stitched", + "numorphstitch/TEST1/stitched/TEST1_0001_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0001_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0002_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0002_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0003_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0003_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0004_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0004_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0005_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0005_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0006_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0006_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0007_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0007_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0008_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0008_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0009_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0009_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0010_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0010_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0011_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0011_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0012_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0012_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0013_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0013_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0014_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0014_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0015_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0015_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0016_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0016_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0017_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0017_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0018_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0018_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/variables", + "numorphstitch/TEST1/variables/adj_params.mat", + "numorphstitch/TEST1/variables/adjusted_z.mat", + "numorphstitch/TEST1/variables/alignment_table.mat", + "numorphstitch/TEST1/variables/path_table.mat", + "numorphstitch/TEST1/variables/stitch_tforms.mat", + "numorphstitch/TEST1/variables/thresholds.mat", + "numorphstitch/TEST1/variables/z_disp_matrix.mat", + "numorphstitch/TEST1/variables/z_displacement_align.mat", "pipeline_info", "unzip", "unzip/TEST1", @@ -318,8 +259,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "25.04.4" + "nextflow": "25.04.6" }, - "timestamp": "2025-06-20T17:44:42.45846679" + "timestamp": "2025-08-29T12:00:50.435832344" } } \ No newline at end of file diff --git a/subworkflows/local/numorph_preprocessing/tests/.nftignore b/subworkflows/local/numorph_preprocessing/tests/.nftignore new file mode 100644 index 0000000..3ebeb10 --- /dev/null +++ b/subworkflows/local/numorph_preprocessing/tests/.nftignore @@ -0,0 +1,20 @@ +.DS_Store +multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt +multiqc/multiqc_data/BETA-multiqc.parquet +multiqc/multiqc_data/multiqc.log +multiqc/multiqc_data/multiqc_data.json +multiqc/multiqc_data/multiqc_sources.txt +multiqc/multiqc_data/multiqc_software_versions.txt +multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} +multiqc/multiqc_report.html +fastqc/*_fastqc.{html,zip} +pipeline_info/*.{html,json,txt,yml} +{numorphintensity,numorphalign,numorphstitch,numorphregister,numorphresample}/*/NM_variables.mat +{numorphintensity,numorphalign,numorphstitch}/*/*/path_table.mat +numorphalign/*/*/alignment_table.mat +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 diff --git a/subworkflows/local/numorph_preprocessing/tests/main.nf.test b/subworkflows/local/numorph_preprocessing/tests/main.nf.test index 50eb47b..0d99077 100644 --- a/subworkflows/local/numorph_preprocessing/tests/main.nf.test +++ b/subworkflows/local/numorph_preprocessing/tests/main.nf.test @@ -15,24 +15,50 @@ nextflow_workflow { test("Numorph Preprocessing") { - options "-stub" + setup { + run ("UNZIP") { + script "../../../../modules/nf-core/unzip/main.nf" + process { + """ + input[0] = Channel.fromList([ + tuple([ id:'TEST1'], + file('https://zenodo.org/records/14916478/files/ctip2_topro.zip')) + ]) + """ + } + } + } when { + params { + outdir = "$outputDir" + } workflow { """ - input[0] = Channel.fromList([ - tuple([ id:'TEST1'], - file('/home/schwitalla/Documents/test-datasets/test_data/images'), - file('test-datasets/test_data/parameterfiles/params_TEST1_lsmquant.csv')) - ]) + input[0] = UNZIP.out.unzipped_archive.map { meta, unzipped_archive -> + tuple( + meta, + unzipped_archive, + file(params.pipelines_testdata_base_path + '/test_data/parameterfiles/params_TEST1_lsmquant.csv')) + } """ } } then { + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'subworkflows/local/numorph_preprocessing/tests/.nftignore') + assert workflow.success assertAll( - { assert workflow.success}, - { assert snapshot(workflow.out).match()} + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + removeNextflowVersion("$outputDir/pipeline_info/nf_core_lsmquant_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name.isEmpty() ? 'No stable paths' : stable_name, + // All files with stable contents + stable_path + ).match()} ) } } diff --git a/subworkflows/local/numorph_preprocessing/tests/main.nf.test.snap b/subworkflows/local/numorph_preprocessing/tests/main.nf.test.snap index 2a3d923..7c2844d 100644 --- a/subworkflows/local/numorph_preprocessing/tests/main.nf.test.snap +++ b/subworkflows/local/numorph_preprocessing/tests/main.nf.test.snap @@ -1,47 +1,514 @@ { "Numorph Preprocessing": { "content": [ - { - "0": [ - [ - { - "id": "TEST1" - }, - "TEST1_stitched.tif:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "thresholds.mat:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "2": [ - "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "3": [ - - ], - "NM_variables": [ - "NM_variables.mat:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "intensity_thresholds": [ - "thresholds.mat:md5,d41d8cd98f00b204e9800998ecf8427e" - ], - "stitched": [ - [ - { - "id": "TEST1" - }, - "TEST1_stitched.tif:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - - ] - } + 7, + null, + [ + "mat2json", + "mat2json/align", + "mat2json/align/NM_variables.json", + "mat2json/align/alignment_table.json", + "mat2json/align/path_table.json", + "mat2json/align/z_displacement_align.json", + "mat2json/intensity", + "mat2json/intensity/NM_variables.json", + "mat2json/intensity/adj_params.json", + "mat2json/intensity/path_table.json", + "mat2json/intensity/thresholds.json", + "mat2json/stitch", + "mat2json/stitch/adj_params.json", + "mat2json/stitch/adjusted_z.csv", + "mat2json/stitch/alignment_table.json", + "mat2json/stitch/path_table.json", + "mat2json/stitch/stitch_tforms.json", + "mat2json/stitch/thresholds.json", + "mat2json/stitch/z_disp_matrix.json", + "mat2json/stitch/z_displacement_align.json", + "numorphalign", + "numorphalign/TEST1", + "numorphalign/TEST1/samples", + "numorphalign/TEST1/samples/alignment", + "numorphalign/TEST1/samples/alignment/TEST1_ctip2_full.tif", + "numorphalign/TEST1/samples/alignment/TEST1_topro_full.tif", + "numorphalign/TEST1/variables", + "numorphalign/TEST1/variables/alignment_table.mat", + "numorphalign/TEST1/variables/path_table.mat", + "numorphalign/TEST1/variables/z_displacement_align.mat", + "numorphintensity", + "numorphintensity/TEST1", + "numorphintensity/TEST1/samples", + "numorphintensity/TEST1/samples/intensity_adjustment", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_2.png", + "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_2.png", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_1_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_2_11.tif", + "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_1.png", + "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_2.png", + "numorphintensity/TEST1/variables", + "numorphintensity/TEST1/variables/adj_params.mat", + "numorphintensity/TEST1/variables/path_table.mat", + "numorphintensity/TEST1/variables/thresholds.mat", + "numorphstitch", + "numorphstitch/TEST1", + "numorphstitch/TEST1/stitched", + "numorphstitch/TEST1/stitched/TEST1_0001_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0001_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0002_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0002_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0003_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0003_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0004_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0004_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0005_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0005_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0006_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0006_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0007_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0007_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0008_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0008_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0009_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0009_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0010_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0010_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0011_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0011_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0012_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0012_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0013_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0013_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0014_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0014_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0015_C1_topro_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0015_C2_ctip2_stitched.tif", + "numorphstitch/TEST1/stitched/TEST1_0016_C1_topro_stitched.tif", + 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@@ -12,9 +12,11 @@ pipeline_info/*.{html,json,txt,yml} {numorphintensity,numorphalign,numorphstitch,numorphregister,numorphresample}/*/NM_variables.mat {numorphintensity,numorphalign,numorphstitch}/*/*/path_table.mat numorphalign/*/*/alignment_table.mat +numorphalign/*/*/z_displacement_align.mat numorphintensity/*/variables/*.mat -numorphintensity/*/samples/*.png +numorphintensity/*/samples/*/*.png numorphstitch/*/variables/*.mat -numorph3dunet/* -mat2json/*/{NM_variables,alignment_table,path_table,adj_params,thresholds, stitch_tforms}.json +numorph3dunet/*/* +mat2json/*/{NM_variables,alignment_table,path_table,adj_params,thresholds,stitch_tforms}.json mat2json/*/*.csv +numorphstitch/*/stitched/TEST1_0006* diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 1607fb1..e40766a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -306,28 +306,18 @@ ], [ "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", - "stitch_tforms.json:md5,b5cc9b439f94631bee62e3f8315dd9aa", "z_disp_matrix.json:md5,575020a27eee808b03c615e0a80ca506", "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", - "TEST1.csv:md5,03ade2aa5a38d978f6b1dd34d741844a", - "TEST1_counts.csv:md5,466295dc5cb794e773520be014ee38ee", "TEST1_ctip2_full.tif:md5,fb17be9f66140c674dad1c0eba3b7a2e", "TEST1_topro_full.tif:md5,5e6784fc7062215bc6538ccccc49a5f4", - "z_displacement_align.mat:md5,39474b8b4f1f246e06f8fb0939989141", "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,d7bb0f7029a40b5a01836a1d76fcc4fe", - "flatfield_2.png:md5,aefc71f6dfef5a51abcfae55547a38b7", - "tile_adj_1.png:md5,2fb1fde009afe7d387d18af329cb5bc8", - "tile_adj_2.png:md5,e7aca3a27fd8df54327192d75e090ed6", "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:md5,4658273b8bd4cd6f8ed8ef86c8b16cf7", - "y_adj_2.png:md5,3426316c88c10efc987d14df902218a8", "TEST1_0001_C1_topro_stitched.tif:md5,317719086b501e2ff598b6378b5000bc", "TEST1_0001_C2_ctip2_stitched.tif:md5,1425cb6fb2329192c34dabc4cdeb608b", "TEST1_0002_C1_topro_stitched.tif:md5,acd2b0c07253e62a51a2211835ee8af3", @@ -338,8 +328,6 @@ "TEST1_0004_C2_ctip2_stitched.tif:md5,42231c67bff5d7051ad9db89deeb0b81", "TEST1_0005_C1_topro_stitched.tif:md5,808ba7185dbfe7acfccf390c64a68df3", "TEST1_0005_C2_ctip2_stitched.tif:md5,529c88a62de7cb8a294c61ee38e43701", - "TEST1_0006_C1_topro_stitched.tif:md5,97b1952d5ae7ab10196a1fe02211db52", - "TEST1_0006_C2_ctip2_stitched.tif:md5,1e18a59e46c87ceec5e6b3e560bbfe59", "TEST1_0007_C1_topro_stitched.tif:md5,7b0f423cdf9bc72519672ddf1a8c9ed2", "TEST1_0007_C2_ctip2_stitched.tif:md5,28cb58d3ded0f479f71de60aee69108b", "TEST1_0008_C1_topro_stitched.tif:md5,fc7b2560cc5f1ba4c335f8a1d7bbad07", @@ -538,6 +526,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-28T18:17:22.248739072" + "timestamp": "2025-08-29T15:05:32.27113918" } } \ No newline at end of file diff --git a/tests/preprocess.nf.test.snap b/tests/preprocess.nf.test.snap index 5233fb0..e958e8d 100644 --- a/tests/preprocess.nf.test.snap +++ b/tests/preprocess.nf.test.snap @@ -299,26 +299,18 @@ ], [ "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", - "stitch_tforms.json:md5,b5cc9b439f94631bee62e3f8315dd9aa", "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:md5,573223719c05fd3f621fadd468c2dabf", "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:md5,1499e8d44ef0fa199d3ae0b0dd8602b3", - "flatfield_2.png:md5,3636cd5855c3c1615e7ad579654183c1", - "tile_adj_1.png:md5,e2032bf09712938c7dd0687570e4548d", - "tile_adj_2.png:md5,aa118ac69fbcc84dfa838a3faf8a973d", "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:md5,6c88c69d4561d4863f26f48bac12fbb6", - "y_adj_2.png:md5,1abf810ab0704628391503922259f826", "TEST1_0001_C1_topro_stitched.tif:md5,317719086b501e2ff598b6378b5000bc", "TEST1_0001_C2_ctip2_stitched.tif:md5,1425cb6fb2329192c34dabc4cdeb608b", "TEST1_0002_C1_topro_stitched.tif:md5,acd2b0c07253e62a51a2211835ee8af3", @@ -329,8 +321,6 @@ "TEST1_0004_C2_ctip2_stitched.tif:md5,42231c67bff5d7051ad9db89deeb0b81", "TEST1_0005_C1_topro_stitched.tif:md5,808ba7185dbfe7acfccf390c64a68df3", "TEST1_0005_C2_ctip2_stitched.tif:md5,529c88a62de7cb8a294c61ee38e43701", - "TEST1_0006_C1_topro_stitched.tif:md5,97b1952d5ae7ab10196a1fe02211db52", - "TEST1_0006_C2_ctip2_stitched.tif:md5,1e18a59e46c87ceec5e6b3e560bbfe59", "TEST1_0007_C1_topro_stitched.tif:md5,7b0f423cdf9bc72519672ddf1a8c9ed2", "TEST1_0007_C2_ctip2_stitched.tif:md5,28cb58d3ded0f479f71de60aee69108b", "TEST1_0008_C1_topro_stitched.tif:md5,fc7b2560cc5f1ba4c335f8a1d7bbad07", @@ -529,6 +519,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-29T10:04:25.997678386" + "timestamp": "2025-08-29T15:22:24.431992314" } } \ No newline at end of file From 0e634df07f8dd5260894716ecf93f7cf16a22863 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Sat, 30 Aug 2025 12:27:41 +0200 Subject: [PATCH 09/27] update test config --- conf/test_gpu.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/conf/test_gpu.config b/conf/test_gpu.config index 9592973..1cda080 100755 --- a/conf/test_gpu.config +++ b/conf/test_gpu.config @@ -14,13 +14,14 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '1.h' + time: '2.h' ] withLabel: process_gpu { ext.use_gpu = true accelerator = 1 containerOptions = { workflow.containerEngine == 'docker' ? '--gpus all' : '--nv' } + memory = { 15.GB * task.attempt } } } From fe77cd446f73ac389b69da9a4b2dc503b5a0dc46 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Sat, 30 Aug 2025 23:14:37 +0200 Subject: [PATCH 10/27] update config --- conf/test_gpu.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_gpu.config b/conf/test_gpu.config index 1cda080..01fc56c 100755 --- a/conf/test_gpu.config +++ b/conf/test_gpu.config @@ -20,7 +20,7 @@ process { withLabel: process_gpu { ext.use_gpu = true accelerator = 1 - containerOptions = { workflow.containerEngine == 'docker' ? '--gpus all' : '--nv' } + // containerOptions = { workflow.containerEngine == 'docker' ? '--gpus all' : '--nv' } memory = { 15.GB * task.attempt } } } From 1c80693a99cae3140f2219299389f45c1479860a Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Mon, 1 Sep 2025 12:17:57 +0200 Subject: [PATCH 11/27] update test profile --- conf/test.config | 9 ++++++++- conf/test_gpu.config | 2 +- nf-test.config | 2 +- tests/default.nf.test | 1 - 4 files changed, 10 insertions(+), 4 deletions(-) diff --git a/conf/test.config b/conf/test.config index b8d58a6..cd7eab9 100755 --- a/conf/test.config +++ b/conf/test.config @@ -16,11 +16,18 @@ process { memory: '15.GB', time: '1.h' ] + + withLabel: process_gpu { + ext.use_gpu = true + accelerator = 1 + // containerOptions = { workflow.containerEngine == 'docker' ? '--gpus all' : '--nv' } + memory = { 15.GB * task.attempt } + } } params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' input = params.pipelines_testdata_base_path + '/test_data/samplesheets/sample_sheet.csv' - stage = 'preprocessing' + stage = 'full' } diff --git a/conf/test_gpu.config b/conf/test_gpu.config index 01fc56c..a0d8b9a 100755 --- a/conf/test_gpu.config +++ b/conf/test_gpu.config @@ -14,7 +14,7 @@ process { resourceLimits = [ cpus: 4, memory: '15.GB', - time: '2.h' + time: '1.h' ] withLabel: process_gpu { diff --git a/nf-test.config b/nf-test.config index 604f3b6..3a1fff5 100644 --- a/nf-test.config +++ b/nf-test.config @@ -12,7 +12,7 @@ config { ignore 'modules/nf-core/**/tests/*', 'subworkflows/nf-core/**/tests/*' // run all test with defined profile(s) from the main nextflow.config - profile "test, docker" + profile "test" // list of filenames or patterns that should be trigger a full test run triggers 'nextflow.config', 'nf-test.config', 'conf/test.config', 'tests/nextflow.config', 'tests/.nftignore' diff --git a/tests/default.nf.test b/tests/default.nf.test index a3b22b9..8b23594 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,7 +4,6 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "gpu" - profile "docker,test_gpu" test("default test gpu") { From a5494c3647f200f3e17d6af4cf61120fca162423 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Mon, 1 Sep 2025 14:05:52 +0200 Subject: [PATCH 12/27] update snapshot pipeline level tests --- tests/default.nf.test | 30 ++ tests/default.nf.test.snap | 84 +++++ tests/preprocess.nf.test | 37 -- tests/preprocess.nf.test.snap | 524 ----------------------------- tests/preprocess_stub.nf.test | 36 -- tests/preprocess_stub.nf.test.snap | 72 ---- 6 files changed, 114 insertions(+), 669 deletions(-) delete mode 100644 tests/preprocess.nf.test delete mode 100644 tests/preprocess.nf.test.snap delete mode 100644 tests/preprocess_stub.nf.test delete mode 100644 tests/preprocess_stub.nf.test.snap diff --git a/tests/default.nf.test b/tests/default.nf.test index 8b23594..f920e00 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -33,4 +33,34 @@ nextflow_pipeline { ) } } + + test("default test gpu -stub") { + + options "-stub" + when { + params { + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_lsmquant_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path + ).match() } + ) + } + } } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e40766a..5dbfce8 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,4 +1,88 @@ { + "default test gpu -stub": { + "content": [ + 8, + { + "MAT2JSON_INT": { + "mat2json": 1.0 + }, + "NUMORPH3DUNET": { + "numorph3dunet": 1.0 + }, + "NUMORPHALIGN": { + "numorphalign": 1.0 + }, + "NUMORPHINTENSITY": { + "numorphintensity": 1.0 + }, + "NUMORPHSTITCH": { + "numorphstitch": 1.0 + }, + "UNZIP": { + "7za": 16.02 + }, + "Workflow": { + "nf-core/lsmquant": "v1.0dev" + } + }, + [ + "mat2json", + "mat2json/align", + "mat2json/align/TEST1.json", + "mat2json/intensity", + "mat2json/intensity/TEST1.json", + "mat2json/stitch", + "mat2json/stitch/TEST1.json", + "numorph3dunet", + "numorph3dunet/TEST1", + "numorph3dunet/TEST1/TEST1.csv", + "numorph3dunet/TEST1/TEST1_counts.csv", + "numorphalign", + "numorphalign/TEST1", + "numorphalign/TEST1/samples", + "numorphalign/TEST1/samples/alignment", + "numorphalign/TEST1/samples/alignment/TEST1_full.tif", + "numorphalign/TEST1/variables", + "numorphalign/TEST1/variables/alignment_table.mat", + "numorphalign/TEST1/variables/path_table.mat", + "numorphalign/TEST1/variables/z_displacement_align.mat", + "numorphintensity", + "numorphintensity/TEST1", + "numorphintensity/TEST1/samples", + "numorphintensity/TEST1/samples/intensity_adjustment", + "numorphintensity/TEST1/samples/intensity_adjustment/TEST1.png", + "numorphintensity/TEST1/variables", + "numorphintensity/TEST1/variables/adj_params.mat", + "numorphintensity/TEST1/variables/path_table.mat", + "numorphintensity/TEST1/variables/thresholds.mat", + "numorphstitch", + "numorphstitch/TEST1", + "numorphstitch/TEST1/stitched", + "numorphstitch/TEST1/stitched/TEST1_stitched.tif", + "numorphstitch/TEST1/variables", + "numorphstitch/TEST1/variables/adjusted_z.mat", + "numorphstitch/TEST1/variables/path_table.mat", + "numorphstitch/TEST1/variables/stitch_tforms.mat", + "numorphstitch/TEST1/variables/z_dips_matrix.mat", + "pipeline_info", + "pipeline_info/nf_core_lsmquant_software_mqc_versions.yml", + "unzip", + "unzip/TEST1" + ], + [ + "TEST1.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "TEST1.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "TEST1.json:md5,d41d8cd98f00b204e9800998ecf8427e", + "TEST1_full.tif:md5,d41d8cd98f00b204e9800998ecf8427e", + "TEST1_stitched.tif:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-09-01T13:52:09.520222007" + }, "default test gpu": { "content": [ 8, diff --git a/tests/preprocess.nf.test b/tests/preprocess.nf.test deleted file mode 100644 index 51d6810..0000000 --- a/tests/preprocess.nf.test +++ /dev/null @@ -1,37 +0,0 @@ -nextflow_pipeline { - - name "Test Workflow main.nf" - script "../main.nf" - tag "cpu" - tag "pipeline_lsmquant" - - - test("-profile test preprocess") { - - when { - params { - outdir = "$outputDir" - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/lsmquant/test_data/samplesheets/sample_sheet.csv' - } - } - - then { - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') - assert workflow.success - assertAll( - { assert snapshot( - // Number of successful tasks - workflow.trace.succeeded().size(), - removeNextflowVersion("$outputDir/pipeline_info/nf_core_lsmquant_software_mqc_versions.yml"), - // All stable path name, with a relative path - stable_name.isEmpty() ? 'No stable paths' : stable_name, - // All files with stable contents - stable_path - ).match()} - ) - } - - } - -} diff --git a/tests/preprocess.nf.test.snap b/tests/preprocess.nf.test.snap deleted file mode 100644 index e958e8d..0000000 --- a/tests/preprocess.nf.test.snap +++ /dev/null @@ -1,524 +0,0 @@ -{ - "-profile test preprocess": { - "content": [ - 7, - { - "MAT2JSON_INT": { - "mat2json": 1.0 - }, - "NUMORPHALIGN": { - "numorphalign": 1.0 - }, - "NUMORPHINTENSITY": { - "numorphintensity": 1.0 - }, - "NUMORPHSTITCH": { - "numorphstitch": 1.0 - }, - "UNZIP": { - "7za": 16.02 - }, - "Workflow": { - "nf-core/lsmquant": "v1.0dev" - } - }, - [ - "mat2json", - "mat2json/align", - "mat2json/align/NM_variables.json", - "mat2json/align/alignment_table.json", - "mat2json/align/path_table.json", - "mat2json/align/z_displacement_align.json", - "mat2json/intensity", - "mat2json/intensity/NM_variables.json", - "mat2json/intensity/adj_params.json", - "mat2json/intensity/path_table.json", - "mat2json/intensity/thresholds.json", - "mat2json/stitch", - "mat2json/stitch/adj_params.json", - "mat2json/stitch/adjusted_z.csv", - "mat2json/stitch/alignment_table.json", - "mat2json/stitch/path_table.json", - "mat2json/stitch/stitch_tforms.json", - "mat2json/stitch/thresholds.json", - "mat2json/stitch/z_disp_matrix.json", - "mat2json/stitch/z_displacement_align.json", - "numorphalign", - "numorphalign/TEST1", - "numorphalign/TEST1/samples", - "numorphalign/TEST1/samples/alignment", - "numorphalign/TEST1/samples/alignment/TEST1_ctip2_full.tif", - "numorphalign/TEST1/samples/alignment/TEST1_topro_full.tif", - "numorphalign/TEST1/variables", - "numorphalign/TEST1/variables/alignment_table.mat", - "numorphalign/TEST1/variables/path_table.mat", - "numorphalign/TEST1/variables/z_displacement_align.mat", - "numorphintensity", - "numorphintensity/TEST1", - "numorphintensity/TEST1/samples", - "numorphintensity/TEST1/samples/intensity_adjustment", - "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_1_11.tif", - "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_1_2_11.tif", - "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_1_11.tif", - "numorphintensity/TEST1/samples/intensity_adjustment/ctip2_2_2_11.tif", - "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_1.png", - "numorphintensity/TEST1/samples/intensity_adjustment/flatfield_2.png", - "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_1.png", - "numorphintensity/TEST1/samples/intensity_adjustment/tile_adj_2.png", - "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_1_11.tif", - "numorphintensity/TEST1/samples/intensity_adjustment/topro_1_2_11.tif", - "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_1_11.tif", - "numorphintensity/TEST1/samples/intensity_adjustment/topro_2_2_11.tif", - "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_1.png", - "numorphintensity/TEST1/samples/intensity_adjustment/y_adj_2.png", - "numorphintensity/TEST1/variables", - "numorphintensity/TEST1/variables/adj_params.mat", - "numorphintensity/TEST1/variables/path_table.mat", - 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] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-08-29T15:22:24.431992314" - } -} \ No newline at end of file diff --git a/tests/preprocess_stub.nf.test b/tests/preprocess_stub.nf.test deleted file mode 100644 index dba49e4..0000000 --- a/tests/preprocess_stub.nf.test +++ /dev/null @@ -1,36 +0,0 @@ -nextflow_pipeline { - - name "Test preprocess workflow stub" - script "../main.nf" - tag "stub" - - - - test("-profile test, stub") { - options "-stub" - - when { - params { - outdir = "$outputDir" - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/lsmquant/test_data/samplesheets/sample_sheet.csv' - } - } - - then { - def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) - def json_files = getAllFilesFromDir(params.outdir, include: ['**/*.json']) - assert workflow.success - assertAll( - { assert snapshot( - // Number of successful tasks - workflow.trace.succeeded().size(), - removeNextflowVersion("$outputDir/pipeline_info/nf_core_lsmquant_software_mqc_versions.yml"), - // All stable path name, with a relative path - stable_name.isEmpty() ? 'No stable paths' : stable_name - ).match()} - ) - } - - } - -} diff --git a/tests/preprocess_stub.nf.test.snap b/tests/preprocess_stub.nf.test.snap deleted file mode 100644 index ac8108f..0000000 --- a/tests/preprocess_stub.nf.test.snap +++ /dev/null @@ -1,72 +0,0 @@ -{ - "-profile test, stub": { - "content": [ - 7, - { - "MAT2JSON_INT": { - "mat2json": 1.0 - }, - "NUMORPHALIGN": { - "numorphalign": 1.0 - }, - "NUMORPHINTENSITY": { - "numorphintensity": 1.0 - }, - "NUMORPHSTITCH": { - "numorphstitch": 1.0 - }, - "UNZIP": { - "7za": 16.02 - }, - "Workflow": { - "nf-core/lsmquant": "v1.0dev" - } - }, - [ - "mat2json", - "mat2json/align", - "mat2json/align/TEST1.json", - "mat2json/intensity", - "mat2json/intensity/TEST1.json", - "mat2json/stitch", - "mat2json/stitch/TEST1.json", - "numorphalign", - "numorphalign/TEST1", - "numorphalign/TEST1/samples", - "numorphalign/TEST1/samples/alignment", - "numorphalign/TEST1/samples/alignment/TEST1_full.tif", - "numorphalign/TEST1/variables", - "numorphalign/TEST1/variables/alignment_table.mat", - "numorphalign/TEST1/variables/path_table.mat", - "numorphalign/TEST1/variables/z_displacement_align.mat", - "numorphintensity", - "numorphintensity/TEST1", - "numorphintensity/TEST1/samples", - "numorphintensity/TEST1/samples/intensity_adjustment", - "numorphintensity/TEST1/samples/intensity_adjustment/TEST1.png", - "numorphintensity/TEST1/variables", - "numorphintensity/TEST1/variables/adj_params.mat", - "numorphintensity/TEST1/variables/path_table.mat", - "numorphintensity/TEST1/variables/thresholds.mat", - "numorphstitch", - "numorphstitch/TEST1", - "numorphstitch/TEST1/stitched", - "numorphstitch/TEST1/stitched/TEST1_stitched.tif", - "numorphstitch/TEST1/variables", - "numorphstitch/TEST1/variables/adjusted_z.mat", - "numorphstitch/TEST1/variables/path_table.mat", - "numorphstitch/TEST1/variables/stitch_tforms.mat", - "numorphstitch/TEST1/variables/z_dips_matrix.mat", - "pipeline_info", - "pipeline_info/nf_core_lsmquant_software_mqc_versions.yml", - "unzip", - "unzip/TEST1" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "25.04.6" - }, - "timestamp": "2025-08-29T09:57:38.849984411" - } -} \ No newline at end of file From 2b2365788abef880c33f32401636a7d717aed915 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Mon, 1 Sep 2025 16:04:31 +0200 Subject: [PATCH 13/27] fix nf-test-gpu.yml --- .github/workflows/nf-test-gpu.yml | 2 +- conf/test.config | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml index 0226dd9..bd068c6 100644 --- a/.github/workflows/nf-test-gpu.yml +++ b/.github/workflows/nf-test-gpu.yml @@ -71,7 +71,7 @@ jobs: needs.get-shards.outputs.total_shards > 0 && ( github.event_name != 'push' || - ( github.event_name == 'push' && github.repository == 'nf-core/methylseq' ) + ( github.event_name == 'push' && github.repository == 'nf-core/lsmquant' ) ) strategy: fail-fast: false diff --git a/conf/test.config b/conf/test.config index cd7eab9..90a81be 100755 --- a/conf/test.config +++ b/conf/test.config @@ -20,7 +20,7 @@ process { withLabel: process_gpu { ext.use_gpu = true accelerator = 1 - // containerOptions = { workflow.containerEngine == 'docker' ? '--gpus all' : '--nv' } + //containerOptions = { workflow.containerEngine == 'docker' ? '--gpus all' : '--nv' } memory = { 15.GB * task.attempt } } } From 4c943b02585519d574d1c36b2b0077e3f61b0116 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Tue, 2 Sep 2025 17:13:15 +0200 Subject: [PATCH 14/27] update modules + container images --- modules/local/mat2json/main.nf | 2 +- modules/local/numorphregister/main.nf | 2 +- modules/local/numorphresample/main.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/local/mat2json/main.nf b/modules/local/mat2json/main.nf index d63de56..cdbd404 100644 --- a/modules/local/mat2json/main.nf +++ b/modules/local/mat2json/main.nf @@ -23,7 +23,7 @@ process MAT2JSON { """ mkdir -p ${process} for matfile in ${matfiles.join(' ')}; do - /usr/bin/mlrtapp/mat2json \$matfile + mat2json \$matfile done mv -f *.json ${process}/ 2>/dev/null || true diff --git a/modules/local/numorphregister/main.nf b/modules/local/numorphregister/main.nf index 4934870..c0fa5f6 100644 --- a/modules/local/numorphregister/main.nf +++ b/modules/local/numorphregister/main.nf @@ -34,7 +34,7 @@ process NUMORPHREGISTER { results="\$PWD/results" - /usr/bin/mlrtapp/numorph_analyze 'input_dir' \$PWD/$resampled_directory 'output_dir' \$PWD/results/ 'parameter_file' $parameter_file 'sample_name' $meta.id 'stage' 'register' 'NM_variables' \$PWD/$nm_variables 'use_processed_images' 'resampled' + numorph_analyze 'input_dir' \$PWD/$resampled_directory 'output_dir' \$PWD/results/ 'parameter_file' $parameter_file 'sample_name' $meta.id 'stage' 'register' 'NM_variables' \$PWD/$nm_variables 'use_processed_images' 'resampled' cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/numorphresample/main.nf b/modules/local/numorphresample/main.nf index 91b79b3..eab2845 100644 --- a/modules/local/numorphresample/main.nf +++ b/modules/local/numorphresample/main.nf @@ -29,7 +29,7 @@ process NUMORPHRESAMPLE { results="\$PWD/results" - /usr/bin/mlrtapp/numorph_analyze 'input_dir' \$PWD/results/stitched 'output_dir' \$results 'parameter_file' $parameter_file 'sample_name' $meta.id 'stage' 'resample' 'NM_variables' \$PWD/$nm_variables 'use_processed_images' 'stitched' + numorph_analyze 'input_dir' \$PWD/results/stitched 'output_dir' \$results 'parameter_file' $parameter_file 'sample_name' $meta.id 'stage' 'resample' 'NM_variables' \$PWD/$nm_variables 'use_processed_images' 'stitched' cat <<-END_VERSIONS > versions.yml "${task.process}": From 8f8b5f1bb5c4cf9909dcecd68a3ba91941d153f1 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Wed, 3 Sep 2025 11:44:07 +0200 Subject: [PATCH 15/27] update nftignore, subworkflow(test) --- .../local/numorph_preprocessing/main.nf | 17 ++++- .../numorph_preprocessing/tests/.nftignore | 1 + .../tests/main.nf.test.snap | 71 +++++++------------ tests/.nftignore | 2 +- tests/default.nf.test.snap | 53 +++----------- 5 files changed, 51 insertions(+), 93 deletions(-) diff --git a/subworkflows/local/numorph_preprocessing/main.nf b/subworkflows/local/numorph_preprocessing/main.nf index 66e9412..b8b8456 100644 --- a/subworkflows/local/numorph_preprocessing/main.nf +++ b/subworkflows/local/numorph_preprocessing/main.nf @@ -5,6 +5,7 @@ include { NUMORPHSTITCH } from '../../../modules/local/nu include { MAT2JSON as MAT2JSON_INT } from '../../../modules/local/mat2json/' include { MAT2JSON as MAT2JSON_ALIGN } from '../../../modules/local/mat2json/' include { MAT2JSON as MAT2JSON_STITCH } from '../../../modules/local/mat2json/' +include { softwareVersionsToYAML } from '../../../subworkflows/nf-core/utils_nfcore_pipeline/' workflow NUMORPH_PREPROCESSING { @@ -78,10 +79,20 @@ workflow NUMORPH_PREPROCESSING { MAT2JSON_STITCH (mat_files_stitch, "stitch" ) ch_versions = ch_versions.mix(MAT2JSON_INT.out.versions) + // Collate and save software versions + // + softwareVersionsToYAML(ch_versions) + .collectFile( + storeDir: "${params.outdir}/pipeline_info", + name: 'nf_core_' + 'lsmquant_software_' + 'mqc_' + 'versions.yml', + sort: true, + newLine: true + ).set { ch_collated_versions } + emit: stitched = stitch_out.stitched // channel: [ path(stitched_dir) ] - intensity_thresholds = intensity_out.thresholds_mat // channel: [path(thresholds_mat) ] - NM_variables = stitch_out.NM_variables // channel: [path(NM_variables) ] - versions = ch_versions // channel: [ versions.yml ] + intensity_thresholds = intensity_out.thresholds_mat // channel: [path(thresholds_mat) ] + NM_variables = stitch_out.NM_variables // channel: [path(NM_variables) ] + versions = ch_collated_versions // channel: [ versions.yml ] } diff --git a/subworkflows/local/numorph_preprocessing/tests/.nftignore b/subworkflows/local/numorph_preprocessing/tests/.nftignore index 3ebeb10..3fbe502 100644 --- a/subworkflows/local/numorph_preprocessing/tests/.nftignore +++ b/subworkflows/local/numorph_preprocessing/tests/.nftignore @@ -18,3 +18,4 @@ numorphstitch/*/variables/*.mat numorph3dunet/* mat2json/*/{NM_variables,alignment_table,path_table,adj_params,thresholds, stitch_tforms}.json mat2json/*/*.csv +numorphstitch/*/stitched/*.{tif,tiff} diff --git a/subworkflows/local/numorph_preprocessing/tests/main.nf.test.snap b/subworkflows/local/numorph_preprocessing/tests/main.nf.test.snap index 7c2844d..80aadd1 100644 --- a/subworkflows/local/numorph_preprocessing/tests/main.nf.test.snap +++ b/subworkflows/local/numorph_preprocessing/tests/main.nf.test.snap @@ -2,7 +2,23 @@ "Numorph Preprocessing": { "content": [ 7, - null, + { + "MAT2JSON_INT": { + "mat2json": 1.0 + }, + "NUMORPHALIGN": { + "numorphalign": 1.0 + }, + "NUMORPHINTENSITY": { + "numorphintensity": 1.0 + }, + "NUMORPHSTITCH": { + "numorphstitch": 1.0 + }, + "Workflow": { + "nf-core/lsmquant": "v1.0dev" + } + }, [ "mat2json", "mat2json/align", @@ -105,6 +121,7 @@ "numorphstitch/TEST1/variables/z_disp_matrix.mat", "numorphstitch/TEST1/variables/z_displacement_align.mat", "pipeline_info", + "pipeline_info/nf_core_lsmquant_software_mqc_versions.yml", "unzip", "unzip/TEST1", "unzip/TEST1/ctip2_topro", @@ -284,57 +301,21 @@ "z_displacement_align.json:md5,0eb5dab0b44ab3c5ceaa8b053ec250e0", "TEST1_ctip2_full.tif:md5,fb17be9f66140c674dad1c0eba3b7a2e", "TEST1_topro_full.tif:md5,5e6784fc7062215bc6538ccccc49a5f4", - "z_displacement_align.mat:md5,3c5408fc956ac909d9f05897ae81c891", + "z_displacement_align.mat:md5,f45d3b73e985017dbfb7c7562bfe5fa4", "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,cabebe657f8d47f1f0268ed2b878e536", - "flatfield_2.png:md5,7946f0e6721852ae88e2a97031bef965", - "tile_adj_1.png:md5,fe7845aaa92cdf1d701096b78de93f8a", - "tile_adj_2.png:md5,06a3cb1c09c6a6dddd23fc536b5cc0af", + "flatfield_1.png:md5,97404fc8aac033969c1911224bf01c20", + "flatfield_2.png:md5,b21b01116bc523cf597915836bf2c42d", + "tile_adj_1.png:md5,b9e6c24c999f7ad9a0b012602b3f1b54", + "tile_adj_2.png:md5,8da66e606f181adf526ab8f1e6e87c50", "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:md5,86a6d9eda5b531b7c064ce49fbf93e66", - "y_adj_2.png:md5,acd862baaf892f48a985dc95ee2bb9f8", - "TEST1_0001_C1_topro_stitched.tif:md5,317719086b501e2ff598b6378b5000bc", - "TEST1_0001_C2_ctip2_stitched.tif:md5,1425cb6fb2329192c34dabc4cdeb608b", - "TEST1_0002_C1_topro_stitched.tif:md5,acd2b0c07253e62a51a2211835ee8af3", - "TEST1_0002_C2_ctip2_stitched.tif:md5,b7836b5a8128d5624370dcff2d856150", - "TEST1_0003_C1_topro_stitched.tif:md5,6933ba04253290df92563ca7325fb5bb", - "TEST1_0003_C2_ctip2_stitched.tif:md5,da0da4d07b03c84ab954b49c4452a43c", - "TEST1_0004_C1_topro_stitched.tif:md5,17380c9c3bd67ea205a8ad69d696f6c6", - "TEST1_0004_C2_ctip2_stitched.tif:md5,42231c67bff5d7051ad9db89deeb0b81", - "TEST1_0005_C1_topro_stitched.tif:md5,808ba7185dbfe7acfccf390c64a68df3", - "TEST1_0005_C2_ctip2_stitched.tif:md5,529c88a62de7cb8a294c61ee38e43701", - "TEST1_0006_C1_topro_stitched.tif:md5,97b1952d5ae7ab10196a1fe02211db52", - "TEST1_0006_C2_ctip2_stitched.tif:md5,1e18a59e46c87ceec5e6b3e560bbfe59", - "TEST1_0007_C1_topro_stitched.tif:md5,7b0f423cdf9bc72519672ddf1a8c9ed2", - "TEST1_0007_C2_ctip2_stitched.tif:md5,28cb58d3ded0f479f71de60aee69108b", - "TEST1_0008_C1_topro_stitched.tif:md5,fc7b2560cc5f1ba4c335f8a1d7bbad07", - "TEST1_0008_C2_ctip2_stitched.tif:md5,f83338d7cc9ad0edf821740a3e099551", - "TEST1_0009_C1_topro_stitched.tif:md5,8577e1c25565d821454a649af56f26a5", - "TEST1_0009_C2_ctip2_stitched.tif:md5,732e3383f5fa11e268b8c06383962cd7", - "TEST1_0010_C1_topro_stitched.tif:md5,1d74b4614291da7c113ca8ccfc401d4f", - "TEST1_0010_C2_ctip2_stitched.tif:md5,4b221f6bdbea74f19a25a7d538706b22", - "TEST1_0011_C1_topro_stitched.tif:md5,878c9f781913909444e9b8c41b1b0d35", - "TEST1_0011_C2_ctip2_stitched.tif:md5,957f0006cdf0ae6042f48ff96f4047b8", - "TEST1_0012_C1_topro_stitched.tif:md5,d4b1f55d2d49d202073914104ca1c6a1", - "TEST1_0012_C2_ctip2_stitched.tif:md5,f822aef32fa1db9adbbfd77874e0677c", - "TEST1_0013_C1_topro_stitched.tif:md5,23f0b137845b4ab97bcadcc8e79a919f", - "TEST1_0013_C2_ctip2_stitched.tif:md5,80ff9f38cf9234528001774382f4517d", - "TEST1_0014_C1_topro_stitched.tif:md5,b9dee935166a2c5b397e26bfc2e1e84a", - "TEST1_0014_C2_ctip2_stitched.tif:md5,13e3b82bb65c1cd731624d523f2eef19", - "TEST1_0015_C1_topro_stitched.tif:md5,92f9c0faa413b03af76aa7927799b66f", - "TEST1_0015_C2_ctip2_stitched.tif:md5,609280edb271acc6820f0deefa0576f7", - "TEST1_0016_C1_topro_stitched.tif:md5,26e73500b59443cb94aa73c0c45f87c6", - "TEST1_0016_C2_ctip2_stitched.tif:md5,ae48a90a29a518e3cd121c91b8e4955c", - "TEST1_0017_C1_topro_stitched.tif:md5,6d9aa1739003ecb59900dad867a094b0", - "TEST1_0017_C2_ctip2_stitched.tif:md5,fb252141f1e9c3344c44acb97bf6b9f6", - "TEST1_0018_C1_topro_stitched.tif:md5,685c86092c751a15c7bc692af8ea9202", - "TEST1_0018_C2_ctip2_stitched.tif:md5,2c559e7593d692e1b399a9de4f83e250", + "y_adj_1.png:md5,d41cf27eb6e3206923ce86957d98802b", + "y_adj_2.png:md5,0d357328a855187c2dce2034834d61bd", "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", @@ -509,6 +490,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-29T10:47:01.7906535" + "timestamp": "2025-09-03T11:10:04.792746217" } } \ No newline at end of file diff --git a/tests/.nftignore b/tests/.nftignore index a96bef9..0cbeb5d 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -19,4 +19,4 @@ numorphstitch/*/variables/*.mat numorph3dunet/*/* mat2json/*/{NM_variables,alignment_table,path_table,adj_params,thresholds,stitch_tforms}.json mat2json/*/*.csv -numorphstitch/*/stitched/TEST1_0006* +numorphstitch/*/stitched/*.{tif,tiff} diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5dbfce8..6c4a8f1 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -6,9 +6,6 @@ "MAT2JSON_INT": { "mat2json": 1.0 }, - "NUMORPH3DUNET": { - "numorph3dunet": 1.0 - }, "NUMORPHALIGN": { "numorphalign": 1.0 }, @@ -18,6 +15,9 @@ "NUMORPHSTITCH": { "numorphstitch": 1.0 }, + "NUMORPH3DUNET": { + "numorph3dunet": 1.0 + }, "UNZIP": { "7za": 16.02 }, @@ -73,15 +73,14 @@ "TEST1.json:md5,d41d8cd98f00b204e9800998ecf8427e", "TEST1.json:md5,d41d8cd98f00b204e9800998ecf8427e", "TEST1.json:md5,d41d8cd98f00b204e9800998ecf8427e", - "TEST1_full.tif:md5,d41d8cd98f00b204e9800998ecf8427e", - "TEST1_stitched.tif:md5,d41d8cd98f00b204e9800998ecf8427e" + "TEST1_full.tif:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-09-01T13:52:09.520222007" + "timestamp": "2025-09-03T11:41:32.289727712" }, "default test gpu": { "content": [ @@ -90,9 +89,6 @@ "MAT2JSON_INT": { "mat2json": 1.0 }, - "NUMORPH3DUNET": { - "numorph3dunet": 1.0 - }, "NUMORPHALIGN": { "numorphalign": 1.0 }, @@ -102,6 +98,9 @@ "NUMORPHSTITCH": { "numorphstitch": 1.0 }, + "NUMORPH3DUNET": { + "numorph3dunet": 1.0 + }, "UNZIP": { "7za": 16.02 }, @@ -402,40 +401,6 @@ "topro_1_2_11.tif:md5,4652de23e14b9b3546c462d18a70e542", "topro_2_1_11.tif:md5,918562924baffc0b99976837ef4b5121", "topro_2_2_11.tif:md5,9f6a1c2b631a11cd675e96fd6e29c1b4", - "TEST1_0001_C1_topro_stitched.tif:md5,317719086b501e2ff598b6378b5000bc", - "TEST1_0001_C2_ctip2_stitched.tif:md5,1425cb6fb2329192c34dabc4cdeb608b", - "TEST1_0002_C1_topro_stitched.tif:md5,acd2b0c07253e62a51a2211835ee8af3", - "TEST1_0002_C2_ctip2_stitched.tif:md5,b7836b5a8128d5624370dcff2d856150", - "TEST1_0003_C1_topro_stitched.tif:md5,6933ba04253290df92563ca7325fb5bb", - "TEST1_0003_C2_ctip2_stitched.tif:md5,da0da4d07b03c84ab954b49c4452a43c", - "TEST1_0004_C1_topro_stitched.tif:md5,17380c9c3bd67ea205a8ad69d696f6c6", - "TEST1_0004_C2_ctip2_stitched.tif:md5,42231c67bff5d7051ad9db89deeb0b81", - "TEST1_0005_C1_topro_stitched.tif:md5,808ba7185dbfe7acfccf390c64a68df3", - "TEST1_0005_C2_ctip2_stitched.tif:md5,529c88a62de7cb8a294c61ee38e43701", - "TEST1_0007_C1_topro_stitched.tif:md5,7b0f423cdf9bc72519672ddf1a8c9ed2", - "TEST1_0007_C2_ctip2_stitched.tif:md5,28cb58d3ded0f479f71de60aee69108b", - "TEST1_0008_C1_topro_stitched.tif:md5,fc7b2560cc5f1ba4c335f8a1d7bbad07", - "TEST1_0008_C2_ctip2_stitched.tif:md5,f83338d7cc9ad0edf821740a3e099551", - "TEST1_0009_C1_topro_stitched.tif:md5,8577e1c25565d821454a649af56f26a5", - "TEST1_0009_C2_ctip2_stitched.tif:md5,732e3383f5fa11e268b8c06383962cd7", - "TEST1_0010_C1_topro_stitched.tif:md5,1d74b4614291da7c113ca8ccfc401d4f", - "TEST1_0010_C2_ctip2_stitched.tif:md5,4b221f6bdbea74f19a25a7d538706b22", - "TEST1_0011_C1_topro_stitched.tif:md5,878c9f781913909444e9b8c41b1b0d35", - "TEST1_0011_C2_ctip2_stitched.tif:md5,957f0006cdf0ae6042f48ff96f4047b8", - "TEST1_0012_C1_topro_stitched.tif:md5,d4b1f55d2d49d202073914104ca1c6a1", - "TEST1_0012_C2_ctip2_stitched.tif:md5,f822aef32fa1db9adbbfd77874e0677c", - "TEST1_0013_C1_topro_stitched.tif:md5,23f0b137845b4ab97bcadcc8e79a919f", - "TEST1_0013_C2_ctip2_stitched.tif:md5,80ff9f38cf9234528001774382f4517d", - "TEST1_0014_C1_topro_stitched.tif:md5,b9dee935166a2c5b397e26bfc2e1e84a", - "TEST1_0014_C2_ctip2_stitched.tif:md5,13e3b82bb65c1cd731624d523f2eef19", - "TEST1_0015_C1_topro_stitched.tif:md5,92f9c0faa413b03af76aa7927799b66f", - "TEST1_0015_C2_ctip2_stitched.tif:md5,609280edb271acc6820f0deefa0576f7", - "TEST1_0016_C1_topro_stitched.tif:md5,26e73500b59443cb94aa73c0c45f87c6", - "TEST1_0016_C2_ctip2_stitched.tif:md5,ae48a90a29a518e3cd121c91b8e4955c", - "TEST1_0017_C1_topro_stitched.tif:md5,6d9aa1739003ecb59900dad867a094b0", - "TEST1_0017_C2_ctip2_stitched.tif:md5,fb252141f1e9c3344c44acb97bf6b9f6", - "TEST1_0018_C1_topro_stitched.tif:md5,685c86092c751a15c7bc692af8ea9202", - "TEST1_0018_C2_ctip2_stitched.tif:md5,2c559e7593d692e1b399a9de4f83e250", "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", @@ -610,6 +575,6 @@ "nf-test": "0.9.2", "nextflow": "25.04.6" }, - "timestamp": "2025-08-29T15:05:32.27113918" + "timestamp": "2025-09-03T11:39:01.448246884" } } \ No newline at end of file From f37b9bbabdc0e1bdfe3486dc1068d0e56fbebff1 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 4 Sep 2025 19:16:10 +0200 Subject: [PATCH 16/27] debug statements --- modules/local/numorph3dunet/main.nf | 6 ++++++ modules/local/numorph3dunet/tests/main.nf.test | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/modules/local/numorph3dunet/main.nf b/modules/local/numorph3dunet/main.nf index c5a02ec..2b1c348 100644 --- a/modules/local/numorph3dunet/main.nf +++ b/modules/local/numorph3dunet/main.nf @@ -25,6 +25,12 @@ process NUMORPH3DUNET { source /opt/conda/etc/profile.d/conda.sh conda activate 3dunet + echo "GPU devices:" + ls -lha /dev/nvidia* || echo "No nvidia devices found" + echo "CUDA_VISIBLE_DEVICES: \$CUDA_VISIBLE_DEVICES" + echo "Checking GPU access:" + nvidia-smi || echo "No nvidia-smi found" + mkdir -p ./results mkdir -p ./images diff --git a/modules/local/numorph3dunet/tests/main.nf.test b/modules/local/numorph3dunet/tests/main.nf.test index 10d1e99..7370db5 100644 --- a/modules/local/numorph3dunet/tests/main.nf.test +++ b/modules/local/numorph3dunet/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "modules_" tag "numorph3dunet" tag "gpu" - profile "docker,gpu" + //profile "docker,gpu" config './nextflow.config' From 7406876a90f4892bf426a16835ec2dfc3a0d1402 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 4 Sep 2025 19:28:54 +0200 Subject: [PATCH 17/27] profile gpu in test file --- modules/local/numorph3dunet/tests/main.nf.test | 2 +- tests/default.nf.test | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/local/numorph3dunet/tests/main.nf.test b/modules/local/numorph3dunet/tests/main.nf.test index 7370db5..3c3f70e 100644 --- a/modules/local/numorph3dunet/tests/main.nf.test +++ b/modules/local/numorph3dunet/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "modules_" tag "numorph3dunet" tag "gpu" - //profile "docker,gpu" + profile "gpu" config './nextflow.config' diff --git a/tests/default.nf.test b/tests/default.nf.test index f920e00..1bf26e8 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,6 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "gpu" + profile 'gpu' test("default test gpu") { From 739331055bf0052c3e2da93b2a238d679686569a Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 4 Sep 2025 19:33:19 +0200 Subject: [PATCH 18/27] profile test,gpu in test file --- tests/default.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 1bf26e8..13f5428 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "gpu" - profile 'gpu' + profile 'test,gpu' test("default test gpu") { From 70c77b5bb2a21f06fa965fdd89198b73ab1e44cb Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 4 Sep 2025 20:20:08 +0200 Subject: [PATCH 19/27] remove nextflow config in test --- modules/local/numorph3dunet/main.nf | 2 +- tests/default.nf.test | 2 +- tests/nextflow.config | 14 -------------- 3 files changed, 2 insertions(+), 16 deletions(-) delete mode 100644 tests/nextflow.config diff --git a/modules/local/numorph3dunet/main.nf b/modules/local/numorph3dunet/main.nf index 2b1c348..5c11e1f 100644 --- a/modules/local/numorph3dunet/main.nf +++ b/modules/local/numorph3dunet/main.nf @@ -27,7 +27,7 @@ process NUMORPH3DUNET { echo "GPU devices:" ls -lha /dev/nvidia* || echo "No nvidia devices found" - echo "CUDA_VISIBLE_DEVICES: \$CUDA_VISIBLE_DEVICES" + echo "Checking GPU access:" nvidia-smi || echo "No nvidia-smi found" diff --git a/tests/default.nf.test b/tests/default.nf.test index 13f5428..654069e 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "gpu" - profile 'test,gpu' + //profile 'test,gpu' test("default test gpu") { diff --git a/tests/nextflow.config b/tests/nextflow.config deleted file mode 100644 index 7370b5e..0000000 --- a/tests/nextflow.config +++ /dev/null @@ -1,14 +0,0 @@ -/* -======================================================================================== - Nextflow config file for running nf-test tests -======================================================================================== -*/ - -// TODO nf-core: Specify any additional parameters here -// Or any resources requirements -params { - modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' - pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/lsmquant' -} - -aws.client.anonymous = true // fixes S3 access issues on self-hosted runners From 669b9ace112a043d8b707f4c66af585df026a850 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 4 Sep 2025 20:29:40 +0200 Subject: [PATCH 20/27] config file --- tests/nextflow.config | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 tests/nextflow.config diff --git a/tests/nextflow.config b/tests/nextflow.config new file mode 100644 index 0000000..b2bb1bf --- /dev/null +++ b/tests/nextflow.config @@ -0,0 +1,24 @@ +/* +======================================================================================== + Nextflow config file for running nf-test tests +======================================================================================== +*/ + +// TODO nf-core: Specify any additional parameters here +// Or any resources requirements +params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/lsmquant' +} + +process { + withLabel: process_gpu { + ext.use_gpu = true + accelerator = 1 + memory = { 15.GB * task.attempt } + } +} + + + +aws.client.anonymous = true // fixes S3 access issues on self-hosted runners From 165b3c4a20c52eeb1752626e44f325a62e720564 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Fri, 5 Sep 2025 10:39:34 +0200 Subject: [PATCH 21/27] add gpu profile to test --- tests/default.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 654069e..1bf26e8 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "gpu" - //profile 'test,gpu' + profile 'gpu' test("default test gpu") { From 4b41cb66c661d2428bc65b7ea298adab352e16df Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Fri, 5 Sep 2025 12:39:41 +0200 Subject: [PATCH 22/27] reset profiles in default test + add svg metromap +hirse promo badge --- README.md | 3 ++- docs/images/lsmquant-metromap.svg | 4 ++++ docs/images/lsmquant.png | Bin 116611 -> 0 bytes tests/default.nf.test | 2 +- 4 files changed, 7 insertions(+), 2 deletions(-) create mode 100644 docs/images/lsmquant-metromap.svg delete mode 100644 docs/images/lsmquant.png diff --git a/README.md b/README.md index c753656..998cd5a 100755 --- a/README.md +++ b/README.md @@ -17,13 +17,14 @@ [![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/lsmquant) [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23lsmquant-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/lsmquant)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) +![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?style=plastic&label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo) ## Introduction **nf-core/lsmquant** is a bioinformatics pipeline that performs preprocessing and analysis of light-sheet microscopy images of tissue cleard samples. The pipeline takes 2D single-channel 16-bit `.tif` images as input. The preprocessing consists of intesity adjustment, channel alignemnt, and tile stitching to reconstruct the 3D image. For mousebrain samples it offers a regsitration to the Allen Mouse Brain Reference Atlas for precise region annotation. Cell nuclei quantification is perfomed on the nuclear channel by a 3D-Unet.
-lasmquant metromap +lasmquant metromap
### Basic workflow diff --git a/docs/images/lsmquant-metromap.svg b/docs/images/lsmquant-metromap.svg new file mode 100644 index 0000000..51d4014 --- /dev/null +++ b/docs/images/lsmquant-metromap.svg @@ -0,0 +1,4 @@ + + + +
Preprocessing workflow
Full workflow
Allen Atlas registration
Intensity
Adjustment
Channel
Alignment
Iterative
Stitching
Segmentation:
Nuclei Quantification
Resampling
ARA 
Registration
mat2json
mat2json
nii
nii
nii
json
resampled
image
Registration
parameters
moving
image
ref
image
tiff
tiff/png
json
intensity
parameters
QC images
mat2json
mat2json
mat2json
tiff
json
Alignment
parameters
aligned
images
tiff
Stitched
images
json
Stitching
parameters
csv
Cell count
table
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zLL?=|qYSCf)E|S&rYE5vbPBlx1g5%&`O~3ncLVNP9f>ToIfoXvBXYiAmX+b2= zFZ2pwxaQcr}c2Z0z_1sTTVeX8YmHMwARPp#RUhvLb zp}xoRI_xV0*zjjBlcRS-Gt7r^sjLn@!;r-Ld+?q%DrB3bMKxM9RI*f~HCrVXn%kjK zI_y)o>w^uc9m5~2hK};RH9~+n1wL{gnEt3luC)+OfaJ{G6BLX}ryjmBc zT8neNfqo#x7uF-xcf*7`pRYLvp(0A!oqz6{{r^|NxPLzMzpwwTPyRJh`G0+JwuwXJ W<7BgZ(dzr)KY5wU(%F)RKK}<)+}^7I diff --git a/tests/default.nf.test b/tests/default.nf.test index 1bf26e8..16ef236 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,7 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "gpu" - profile 'gpu' + test("default test gpu") { From 27f44f1705a40d0cbdeebf3ebde2bb05adb86ad5 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 11 Sep 2025 10:38:44 +0200 Subject: [PATCH 23/27] profile test in test script, deleted obsolete config test_gpu --- conf/test_gpu.config | 34 ---------------------------------- tests/default.nf.test | 1 + tests/nextflow.config | 2 -- 3 files changed, 1 insertion(+), 36 deletions(-) delete mode 100755 conf/test_gpu.config diff --git a/conf/test_gpu.config b/conf/test_gpu.config deleted file mode 100755 index a0d8b9a..0000000 --- a/conf/test_gpu.config +++ /dev/null @@ -1,34 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run nf-core/lsmquant -profile test_gpu, --outdir - ----------------------------------------------------------------------------------------- -*/ - -process { - resourceLimits = [ - cpus: 4, - memory: '15.GB', - time: '1.h' - ] - - withLabel: process_gpu { - ext.use_gpu = true - accelerator = 1 - // containerOptions = { workflow.containerEngine == 'docker' ? '--gpus all' : '--nv' } - memory = { 15.GB * task.attempt } - } -} - -params { - config_profile_name = 'Test profile GPU' - config_profile_description = 'Minimal test dataset to check pipeline function' - // Define the input data - input = params.pipelines_testdata_base_path + '/test_data/samplesheets/sample_sheet.csv' - stage = 'full' -} diff --git a/tests/default.nf.test b/tests/default.nf.test index 16ef236..292c7b7 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -4,6 +4,7 @@ nextflow_pipeline { script "../main.nf" tag "pipeline" tag "gpu" + profile "test" test("default test gpu") { diff --git a/tests/nextflow.config b/tests/nextflow.config index b2bb1bf..89ab0c9 100644 --- a/tests/nextflow.config +++ b/tests/nextflow.config @@ -19,6 +19,4 @@ process { } } - - aws.client.anonymous = true // fixes S3 access issues on self-hosted runners From 7fdbd45d4f4348da6f71f9eb1b93c390964b57f0 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 11 Sep 2025 10:39:58 +0200 Subject: [PATCH 24/27] lint --- ro-crate-metadata.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 8ffc012..9dffaa6 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2025-07-08T11:38:54+00:00", - "description": "

\n \n \n \"nf-core/lsmquant\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/lsmquant/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/lsmquant/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/lsmquant/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/lsmquant/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/lsmquant/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/lsmquant)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23lsmquant-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/lsmquant)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/lsmquant** is a bioinformatics pipeline that performs preprocessing and analysis of light-sheet microscopy images of tissue cleard samples. The pipeline takes 2D single-channel 16-bit `.tif` images as input. The preprocessing consists of intesity adjustment, channel alignemnt, and tile stitching to reconstruct the 3D image. For mousebrain samples it offers a regsitration to the Allen Mouse Brain Reference Atlas for precise region annotation. Cell nuclei quantification is perfomed on the nuclear channel by a 3D-Unet.\n\n
\n\"lasmquant\n
\n\n### Basic workflow\n\n**Preprocessing**\n\n1. Intensity Adjustment\n2. Channel Alignment\n3. Iterative Stitching\n\n**Analysis**\n\n4. ARA Registration subworkflow (optional)\n5. Cell Nuclei Quantification\n\n## Pipeline Summary\n\nThe pipeline consists of two major stages, the `preprocessing`stage and the `analysis`stage.\n\n### Preprocessing\n\nPreprocessing is performed on raw 2D single-channel 16-bit `.tif` images produced by a light sheet microscope. Three individual steps are perfomed :\n\n- Measuring and adjustemnts for intensities\n- Image channel alignemnt for at least two different channels\n- Image tile stitching to recustruct the full image for each channel and z-slice\n\n### Analysis\n\nAnalysis is performed using a 3D-Unet to qunatify the amount of cell-nuclei in the given sample. The quantification is performed on the nuclear channel only, assuming that the corresponding image file names contain the pattern `C1`.\n\nOptionally registration to the Allen Refernce Atlas (ARA) for functional brain region annotation can be perfomed before segmentation.\nThis includes the following two steps:\n\n- Downsampling of the high resolution stitched images\n- Registration to the ARA\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nTo run the pipeline you need to provide a samplesheet with your data in the following structure:\n\n`samplesheet.csv`\n\n```bash\nsample_id,img_directory,parameter_file\nTEST1,path/to/image-files,path/to/parameter/file.csv\n```\n\nThe parameter csv file includes sample specific parameters that are used for processing the given data.It needs to follow a specific structure.\n\nPlease get the basic tempalte file here ( include maybe link to template csv which can be found in the repo ?)\n`parametersheet.csv`\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/lsmquant \\\n -profile \\\n --input \\\n --outdir \\\n --stage \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/lsmquant/usage) and the [parameter documentation](https://nf-co.re/lsmquant/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/lsmquant/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/lsmquant/output).\n\n## Credits\n\nnf-core/lsmquant was originally written by Carolin Schwitalla.\n\nThe pipeline is mainly based on the NuMorph (Nuclear-Based Morphometry) toolbox developed by Krupa et al., 2021.\n\n> **NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images**\n>\n> Krupa O, Fragola G, Hadden-Ford E, Mory JT, Liu T, Humphrey Z, Rees BW, Krishnamurthy A, Snider WD, Zylka MJ, Wu G, Xing L, Stein JL.\n>\n> Cell Rep. 2021 Oct 12, doi: [10.1016/j.celrep.2021.109802](https://doi.org/10.1016%2Fj.celrep.2021.109802)\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#lsmquant` channel](https://nfcore.slack.com/channels/lsmquant) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "description": "

\n \n \n \"nf-core/lsmquant\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/lsmquant/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/lsmquant/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/lsmquant/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/lsmquant/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/lsmquant/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/lsmquant)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23lsmquant-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/lsmquant)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)\n![HiRSE Code Promo Badge](https://img.shields.io/badge/Promo-8db427?style=plastic&label=HiRSE&labelColor=005aa0&link=https%3A%2F%2Fgo.fzj.de%2FCodePromo)\n\n## Introduction\n\n**nf-core/lsmquant** is a bioinformatics pipeline that performs preprocessing and analysis of light-sheet microscopy images of tissue cleard samples. The pipeline takes 2D single-channel 16-bit `.tif` images as input. The preprocessing consists of intesity adjustment, channel alignemnt, and tile stitching to reconstruct the 3D image. For mousebrain samples it offers a regsitration to the Allen Mouse Brain Reference Atlas for precise region annotation. Cell nuclei quantification is perfomed on the nuclear channel by a 3D-Unet.\n\n
\n\"lasmquant\n
\n\n### Basic workflow\n\n**Preprocessing**\n\n1. Intensity Adjustment\n2. Channel Alignment\n3. Iterative Stitching\n\n**Analysis**\n\n4. ARA Registration subworkflow (optional)\n5. Cell Nuclei Quantification\n\n## Pipeline Summary\n\nThe pipeline consists of two major stages, the `preprocessing`stage and the `analysis`stage.\n\n### Preprocessing\n\nPreprocessing is performed on raw 2D single-channel 16-bit `.tif` images produced by a light sheet microscope. Three individual steps are perfomed :\n\n- Measuring and adjustemnts for intensities\n- Image channel alignemnt for at least two different channels\n- Image tile stitching to recustruct the full image for each channel and z-slice\n\n### Analysis\n\nAnalysis is performed using a 3D-Unet to qunatify the amount of cell-nuclei in the given sample. The quantification is performed on the nuclear channel only, assuming that the corresponding image file names contain the pattern `C1`.\n\nOptionally registration to the Allen Refernce Atlas (ARA) for functional brain region annotation can be perfomed before segmentation.\nThis includes the following two steps:\n\n- Downsampling of the high resolution stitched images\n- Registration to the ARA\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nTo run the pipeline you need to provide a samplesheet with your data in the following structure:\n\n`samplesheet.csv`\n\n```bash\nsample_id,img_directory,parameter_file\nTEST1,path/to/image-files,path/to/parameter/file.csv\n```\n\nThe parameter csv file includes sample specific parameters that are used for processing the given data.It needs to follow a specific structure.\n\nPlease get the basic tempalte file here ( include maybe link to template csv which can be found in the repo ?)\n`parametersheet.csv`\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/lsmquant \\\n -profile \\\n --input \\\n --outdir \\\n --stage \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/lsmquant/usage) and the [parameter documentation](https://nf-co.re/lsmquant/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/lsmquant/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/lsmquant/output).\n\n## Credits\n\nnf-core/lsmquant was originally written by Carolin Schwitalla.\n\nThe pipeline is mainly based on the NuMorph (Nuclear-Based Morphometry) toolbox developed by Krupa et al., 2021.\n\n> **NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images**\n>\n> Krupa O, Fragola G, Hadden-Ford E, Mory JT, Liu T, Humphrey Z, Rees BW, Krishnamurthy A, Snider WD, Zylka MJ, Wu G, Xing L, Stein JL.\n>\n> Cell Rep. 2021 Oct 12, doi: [10.1016/j.celrep.2021.109802](https://doi.org/10.1016%2Fj.celrep.2021.109802)\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#lsmquant` channel](https://nfcore.slack.com/channels/lsmquant) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" From 61f7e6d9e6c563c5971965792a71b04ca5ab64a1 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 11 Sep 2025 14:27:25 +0200 Subject: [PATCH 25/27] add nextflow debug var and get conatiner launch information... --- .github/workflows/nf-test-gpu.yml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml index bd068c6..c8a29c1 100644 --- a/.github/workflows/nf-test-gpu.yml +++ b/.github/workflows/nf-test-gpu.yml @@ -88,6 +88,13 @@ jobs: with: fetch-depth: 0 + - name: Test CUDA + run: | + nvidia-smi -L + + - name: Enable Nextflow debug logging + run: echo "NXF_DEBUG=2" >> $GITHUB_ENV + - name: Run nf-test Action uses: ./.github/actions/nf-test with: @@ -97,6 +104,10 @@ jobs: filters: ${{ matrix.filters }} tags: "gpu" + - name: Show Singularity run commands + run: | + grep "singularity exec" .nextflow.log || echo "No singularity exec found" + confirm-pass: runs-on: - runs-on=${{ github.run_id }}-confirm-pass From afd820f883c96dfc1edf0240ddce2c394855b222 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Thu, 11 Sep 2025 14:59:13 +0200 Subject: [PATCH 26/27] find nextflow log on ci --- .github/workflows/nf-test-gpu.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/nf-test-gpu.yml b/.github/workflows/nf-test-gpu.yml index c8a29c1..8b9d2ba 100644 --- a/.github/workflows/nf-test-gpu.yml +++ b/.github/workflows/nf-test-gpu.yml @@ -106,7 +106,7 @@ jobs: - name: Show Singularity run commands run: | - grep "singularity exec" .nextflow.log || echo "No singularity exec found" + find . -name ".nextflow.log" -exec grep "singularity exec" {} + || echo "No singularity exec found" confirm-pass: runs-on: From 4159eeb3ec528b4d629ed2de1b5737e819789439 Mon Sep 17 00:00:00 2001 From: CaroAMN Date: Mon, 22 Sep 2025 17:02:13 +0200 Subject: [PATCH 27/27] removed pwd + resolved symlinks for registration and resampling modules + removed unused container options in test.config --- conf/test.config | 1 - modules/local/numorphregister/main.nf | 8 ++++++-- modules/local/numorphresample/main.nf | 12 ++++++++---- 3 files changed, 14 insertions(+), 7 deletions(-) diff --git a/conf/test.config b/conf/test.config index 90a81be..ae77f99 100755 --- a/conf/test.config +++ b/conf/test.config @@ -20,7 +20,6 @@ process { withLabel: process_gpu { ext.use_gpu = true accelerator = 1 - //containerOptions = { workflow.containerEngine == 'docker' ? '--gpus all' : '--nv' } memory = { 15.GB * task.attempt } } } diff --git a/modules/local/numorphregister/main.nf b/modules/local/numorphregister/main.nf index c0fa5f6..48fcdbd 100644 --- a/modules/local/numorphregister/main.nf +++ b/modules/local/numorphregister/main.nf @@ -32,9 +32,13 @@ process NUMORPHREGISTER { mv $resampled_directory \$PWD/results/resampled - results="\$PWD/results" + #resolve symlinks and paths + resampled_directory=\$(readlink -f ./results/resampled/) + parameter_file=\$(readlink -f ${parameter_file}) + NM_variables=\$(readlink -f ${NM_variables}) + results_dir=\$(readlink -f ./results) - numorph_analyze 'input_dir' \$PWD/$resampled_directory 'output_dir' \$PWD/results/ 'parameter_file' $parameter_file 'sample_name' $meta.id 'stage' 'register' 'NM_variables' \$PWD/$nm_variables 'use_processed_images' 'resampled' + numorph_analyze 'input_dir' \$resampled_directory 'output_dir' \$results_dir 'parameter_file' \$parameter_file 'sample_name' ${meta.id} 'stage' 'register' 'NM_variables' \$NM_variables 'use_processed_images' 'resampled' cat <<-END_VERSIONS > versions.yml diff --git a/modules/local/numorphresample/main.nf b/modules/local/numorphresample/main.nf index eab2845..ec6c3fe 100644 --- a/modules/local/numorphresample/main.nf +++ b/modules/local/numorphresample/main.nf @@ -23,13 +23,17 @@ process NUMORPHRESAMPLE { def nm_variables = NM_variables ? "${NM_variables}" : "" """ - mkdir -p \$PWD/results/stitched/ + mkdir -p results/stitched/ - mv $stitch_directory \$PWD/results/stitched + mv $stitch_directory results/stitched - results="\$PWD/results" + # resolve symlinks and paths + stitch_directory=\$(readlink -f ./results/stitched/) + parameter_file=\$(readlink -f ${parameter_file}) + NM_variables=\$(readlink -f ${NM_variables}) + results_dir=\$(readlink -f ./results) - numorph_analyze 'input_dir' \$PWD/results/stitched 'output_dir' \$results 'parameter_file' $parameter_file 'sample_name' $meta.id 'stage' 'resample' 'NM_variables' \$PWD/$nm_variables 'use_processed_images' 'stitched' + numorph_analyze 'input_dir' \$stitch_directory 'output_dir' \$results_dir 'parameter_file' \$parameter_file 'sample_name' ${meta.id} 'stage' 'resample' 'NM_variables' \$NM_variables 'use_processed_images' 'stitched' cat <<-END_VERSIONS > versions.yml "${task.process}":