Merge pull request #54 from CaroAMN/dev

Adding Review feedback

Author: CaroAMN

assets/numorph_params_schema.json

@@ -1,5 +1,19 @@
 Parameter,Value
+group,TEST;WT;R1
+channel_num,C01;C00
+markers,topro;ctip2
+position_exp,[\d*;\d*];Z\d*
+resolution,1.2100;1.2100;4
+orientation,ail
+hemisphere,both
+use_processed_images,false
+ignore_markers,Auto
+save_images,true
+save_samples,true
+adjust_intensity,true
 darkfield_intensity,101
+adjust_tile_shading,basic
+adjust_tile_position,true
 update_intensity_channels,
 single_sheet,true
 ls_width,50
@@ -8,14 +22,15 @@ sampling_frequency,0.2
 shading_correction_tiles,
 shading_smoothness,2
 shading_intensity,1
-update_z_adjustment,false
-z_positions,0.01
-z_window,5
-z_initial,0
+channel_alignment,update
 align_method,translation
 align_tiles,
 align_channels,
 align_slices,
+update_z_adjustment,false
+z_positions,0.01
+z_window,5
+z_initial,0
 align_stepsize,5
 only_pc,false
 align_chunks,
@@ -26,6 +41,7 @@ chunk_pad,30
 mask_int_threshold,
 resample_s,3;3;1
 hist_match,64
+stitch_images,true
 sift_refinement,true
 load_alignment_params,true
 overlap,0.20
@@ -49,28 +65,10 @@ smooth_img,false
 smooth_sigma,
 flip_axis,none
 rotate_axis,0
-group,TEST;WT;R1
-channel_num,C01;C00
-markers,topro;ctip2
-position_exp,[\d*;\d*];Z\d*
-resolution,1.2100;1.2100;4
-overlap,0.15
-orientation,ail
-hemisphere,both
-channel_alignment,update
-adjust_intensity,true
-stitch_images,true
-use_processed_images,false
-ignore_markers,Auto
-save_images,true
-save_samples,true
-adjust_tile_shading,basic
-adjust_tile_position,true
 resample_images,true
 register_images,true
 count_nuclei,true
 classify_cells,true
-use_processed_images,false
 resample_resolution,25
 resample_channels,
 use_annotation_mask,false
@@ -103,4 +101,3 @@ measure_coloc,
 n_channels,
 use_mask,
 mask_file,
-resample_resolution,

assets/params_template_lsmquant.csv

@@ -33,14 +33,14 @@ process {
         ]
     }
 
-    withName: 'NUMORPHINTENSITY' {
+    withName: 'NUMORPH_INTENSITY' {
         cpus   = { 2     * task.attempt }
         memory = { 30.GB * task.attempt }
         time   = { 2.h  * task.attempt  }
         publishDir = [
-            path: { "${params.outdir}/numorphintensity/" },
+            path: { "${params.outdir}/numorph_intensity" },
             mode: params.publish_dir_mode,
-            pattern: 'results/**/*',
+            pattern: 'results/**',
             saveAs: { filename ->
                 if (filename.equals('versions.yml')) {
                     null
@@ -87,9 +87,9 @@ process {
         ]
     }
 
-    withName: 'NUMORPHRESAMPLE' {
+    withName: 'NUMORPH_RESAMPLE' {
         publishDir = [
-            path: { "${params.outdir}/numorphresample/" },
+            path: { "${params.outdir}/numorph_resample/" },
             mode: params.publish_dir_mode,
             pattern: 'results/**/*',
             saveAs: { filename ->

conf/modules.config

@@ -5,17 +5,27 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "mat2json": {
+                        "branch": "master",
+                        "git_sha": "163b8a7181a343e98a292c626889a81d2da90298",
+                        "installed_by": ["modules"]
+                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
                         "installed_by": ["modules"]
                     },
-                    "unzip": {
+                    "numorph/intensity": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "163b8a7181a343e98a292c626889a81d2da90298",
                         "installed_by": ["modules"]
                     },
-                    "unzipfiles": {
+                    "numorph/resample": {
+                        "branch": "master",
+                        "git_sha": "380cb90926b8c28558cb11479da5ff45bc4f1c5d",
+                        "installed_by": ["modules"]
+                    },
+                    "unzip": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]

docs/usage.md

@@ -9,8 +9,9 @@ process NUMORPH3DUNET {
     path(model_file)
 
     output:
-    path "${prefix}/*"              , emit: cellcounts
-    path "versions.yml"             , emit: versions
+    tuple val(meta), path ("${prefix}/")              , emit: cellcounts
+
+    tuple val("${task.process}"), val('numorph-3dunet'), val('1.0.0'), emit: versions_numorph_3dunet, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -38,10 +39,6 @@ process NUMORPH3DUNET {
         --sample_id ${prefix} \\
         $args
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        numorph3dunet: 1.0
-    END_VERSIONS
     """
 
     stub:
@@ -53,9 +50,5 @@ process NUMORPH3DUNET {
     touch ${prefix}/${prefix}.csv
     touch ${prefix}/${prefix}_counts.csv
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        numorph3dunet: 1.0
-    END_VERSIONS
     """
 }

modules.json

@@ -12,7 +12,7 @@ nextflow_process {
 
     config './nextflow.config'
 
-    test("Numorph3DUnet test - tif") {
+    test("numorph-3DUnet test - tif") {
 
         setup {
             run ("UNZIP") {
@@ -30,7 +30,7 @@ nextflow_process {
 
         when {
             params {
-                outdir = "$workDir/output"
+                outdir = "$outputDir"
             }
             process {
                 """
@@ -47,13 +47,21 @@ nextflow_process {
         }
 
         then {
-            assert process.success              // Check process completed successfully
-            assert snapshot(process.out).match() // Validate outputs match expected snapshot
+            def cellcounDir = process.out.cellcounts.get(0).get(1)
+            def cellcountFiles = getAllFilesFromDir(cellcounDir, relative: true, includeDir: false)
+            assertAll(
+                {assert process.success },
+                {assert cellcountFiles.size() == 2 },
+                { assert snapshot(
+                    cellcountFiles,
+                    process.out.versions
+                ).match() }
+            )
         }
 
     }
 
-    test("Numorph3DUnet stub test - tif") {
+    test("numorph-3DUnet stub test - tif") {
 
         options '-stub'
 

modules/local/numorph3dunet/main.nf

@@ -1,57 +1,60 @@
 {
-    "Numorph3DUnet test - tif": {
+    "numorph-3DUnet test - tif": {
         "content": [
-            {
-                "0": [
-                    [
-                        "TEST1.csv:md5,fa930f84f08fa69d825bca59cc08dcec",
-                        "TEST1_counts.csv:md5,6f482bb276d66163f0646ba6d4712075"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,a48272c66a933f2bbbaa710df8129f03"
-                ],
-                "cellcounts": [
-                    [
-                        "TEST1.csv:md5,fa930f84f08fa69d825bca59cc08dcec",
-                        "TEST1_counts.csv:md5,6f482bb276d66163f0646ba6d4712075"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,a48272c66a933f2bbbaa710df8129f03"
-                ]
-            }
+            [
+                "TEST1.csv",
+                "TEST1_counts.csv"
+            ],
+            null
         ],
-        "timestamp": "2026-02-28T16:52:51.765396671",
+        "timestamp": "2026-03-18T09:39:51.811502005",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.3"
         }
     },
-    "Numorph3DUnet stub test - tif": {
+    "numorph-3DUnet stub test - tif": {
         "content": [
             {
                 "0": [
                     [
-                        "TEST1.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "TEST1_counts.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        {
+                            "id": "TEST1"
+                        },
+                        [
+                            "TEST1.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "TEST1_counts.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,a48272c66a933f2bbbaa710df8129f03"
+                    [
+                        "NUMORPH3DUNET",
+                        "numorph-3dunet",
+                        "1.0.0"
+                    ]
                 ],
                 "cellcounts": [
                     [
-                        "TEST1.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
-                        "TEST1_counts.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        {
+                            "id": "TEST1"
+                        },
+                        [
+                            "TEST1.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "TEST1_counts.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,a48272c66a933f2bbbaa710df8129f03"
+                "versions_numorph_3dunet": [
+                    [
+                        "NUMORPH3DUNET",
+                        "numorph-3dunet",
+                        "1.0.0"
+                    ]
                 ]
             }
         ],
-        "timestamp": "2026-03-03T15:01:48.714597704",
+        "timestamp": "2026-03-18T09:40:24.396612007",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.3"

modules/local/numorph3dunet/tests/main.nf.test

@@ -6,20 +6,16 @@ process NUMORPHALIGN {
     container "nf-core/numorph_preprocessing:1.0.0"
 
     input:
-    tuple val(meta), path(img_directory),  path(parameter_file)
-    path adj_params_mat
-    path path_table_mat
-    path thresholds_mat
-    path NM_variables
+    tuple val(meta), path(img_directory),  path(parameter_file), path(variables), path(NM_variable)
 
 
     output:
-    path "./results/samples/alignment/"                     , emit: samples
-    path "./results/variables/path_table.mat"               , emit: path_table_mat
-    path "./results/variables/alignment_table.mat"          , emit: alignment_table_mat
-    path "./results/variables/z_displacement_align.mat"     , emit: z_displacement_align_mat
-    path "./results/NM_variables.mat"                       , emit: NM_variables
-    path "versions.yml"                                     , emit: versions
+    tuple val(meta), path("./results/samples/alignment/")                     , emit: samples_alignment
+    tuple val(meta), path("./results/variables/")                             , emit: variables_alignment
+    tuple val(meta), path("./results/NM_variables.mat")                       , emit: NM_variable
+
+    tuple val("${task.process}"), val('numorph_align'), val('1.0.0'), emit: versions_numorph_align, topic: versions
+
 
 
     when:
@@ -32,27 +28,20 @@ process NUMORPHALIGN {
     """
     # create output directories needed by the tool
     mkdir -p ./results/samples/
-    mkdir -p ./results/variables/
+
 
 
     # symlink input files to variables directory
-    ln -sr ${adj_params_mat} ./results/variables
-    ln -sr ${path_table_mat} ./results/variables
-    ln -sr ${thresholds_mat} ./results/variables
+    cp -rL ${variables} ./results
 
-    # resolve symlinks and paths
+    # resolve symlinks and paths for matlab tool
     img_dir=\$(readlink -f ${img_directory})
     parameter_file=\$(readlink -f ${parameter_file})
     results_dir=\$(readlink -f ./results)
-    NM_variables=\$(readlink -f ${NM_variables})
+    NM_variables=\$(readlink -f ${NM_variable})
 
     numorph_preprocessing 'input_dir' \$img_dir 'output_dir' \$results_dir 'parameter_file' \$parameter_file 'sample_name' ${meta.id} 'stage' 'align' 'NM_variables' \$NM_variables
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        numorphalign: 1.0
-    END_VERSIONS
-
     """
 
     stub:
@@ -69,9 +58,5 @@ process NUMORPHALIGN {
     touch results/NM_variables.mat
     touch results/samples/alignment/${meta.id}_full.tif
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        numorphalign: 1.0
-    END_VERSIONS
     """
 }