bug fix for issue nf-core#27; split basicpy output by ID

RobJY · May 8, 2024 · f26879f · f26879f
1 parent c0689fa
commit f26879f
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Showing 5 changed files with 89 additions and 31 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -32,7 +32,13 @@ process {
         publishDir = [
             path: { "${params.outdir}/illumination_correction/basicpy" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename ->
+                if (filename.equals('versions.yml')) {
+                    filename
+                } else {
+                    meta.id + "_" + filename
+                }
+            }
         ]
     }
 

diff --git a/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf b/subworkflows/local/utils_nfcore_mcmicro_pipeline/main.nf
@@ -262,7 +262,7 @@ def validateInputSamplesheetRow ( row, mode ) {
     if (mode == "sample") {
         // check for the existence of all files under cycle_image column in the given image_directory
         if (row.size() >= 3 && row[2] != []) {
-            def file_list = row[2].split(" ")
+            def file_list = row[2].split(";")
             file_list.each { curr_file ->
                 def curr_path = file(row[1].toString() + "/" + curr_file)
                 if (!curr_path.exists()) {
@@ -315,7 +315,7 @@ def make_ashlar_input_sample( samplesheet_row ) {
         if (tmp_path[-1] != "/") {
             tmp_path = "${tmp_path}/"
         }
-        cycle_images = samplesheet_row[index_sample_cycle_images].split(' ').collect{ "${tmp_path}${it}" }
+        cycle_images = samplesheet_row[index_sample_cycle_images].split(';').collect{ "${tmp_path}${it}" }
         cycle_images.each{ file_path ->
             def file_test = file(file_path)
             if (!file_test.exists()) {

diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -92,8 +92,8 @@ nextflow_workflow {
                             ImageUtils.getImageMetadata("$outputDir/registration/ashlar/TEST1.ome.tif"),
                             ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
                             CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/TEST1_mask_TEST1.csv"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff")
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST1_cycif-tonsil-cycle1.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST1_cycif-tonsil-cycle1.ome-ffp.tiff")
                         ).match()
                     },
                     { assert workflow.success }
@@ -308,12 +308,12 @@ nextflow_workflow {
                             ImageUtils.getImageMetadata("$outputDir/registration/ashlar/cycif-tonsil.ome.tif"),
                             ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil.tif"),
                             CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/cycif-tonsil_mask_cycif-tonsil.csv"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-ffp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle3.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle3.ome-ffp.tiff")
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil_cycif-tonsil-cycle1.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil_cycif-tonsil-cycle1.ome-ffp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil_cycif-tonsil-cycle2.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil_cycif-tonsil-cycle2.ome-ffp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil_cycif-tonsil-cycle3.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil_cycif-tonsil-cycle3.ome-ffp.tiff")
                         ).match()
                     },
                     { assert workflow.success }
@@ -362,12 +362,14 @@ nextflow_workflow {
                             path("$outputDir/segmentation/deepcell_mesmer/mask_cycif-tonsil2.tif"),
                             CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/cycif-tonsil_mask_cycif-tonsil.csv"),
                             CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/cycif-tonsil2_mask_cycif-tonsil2.csv"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-ffp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle3.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle3.ome-ffp.tiff")
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil_cycif-tonsil-cycle1.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil_cycif-tonsil-cycle1.ome-ffp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil_cycif-tonsil-cycle2.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil_cycif-tonsil-cycle2.ome-ffp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil2_cycif-tonsil-cycle2.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil2_cycif-tonsil-cycle2.ome-ffp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil2_cycif-tonsil-cycle3.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil2_cycif-tonsil-cycle3.ome-ffp.tiff")
                         ).match()
                     },
                     { assert workflow.success }
@@ -441,10 +443,10 @@ nextflow_workflow {
                             ImageUtils.getImageMetadata("$outputDir/registration/ashlar/TEST1.ome.tif"),
                             ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_TEST1.tif"),
                             CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/TEST1_mask_TEST1.csv"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-ffp.tiff")
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST1_cycif-tonsil-cycle1.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST1_cycif-tonsil-cycle1.ome-ffp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST1_cycif-tonsil-cycle2.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST1_cycif-tonsil-cycle2.ome-ffp.tiff")
                         ).match()
                     },
                     { assert workflow.success }
@@ -495,12 +497,14 @@ nextflow_workflow {
                             ImageUtils.getImageMetadata("$outputDir/segmentation/deepcell_mesmer/mask_TEST2.tif"),
                             CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/TEST1_mask_TEST1.csv"),
                             CsvUtils.summarizeCsv("$outputDir/quantification/mcquant/TEST2_mask_TEST2.csv"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle1.ome-ffp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle2.ome-ffp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle3.ome-dfp.tiff"),
-                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/cycif-tonsil-cycle3.ome-ffp.tiff")
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST1_cycif-tonsil-cycle1.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST1_cycif-tonsil-cycle1.ome-ffp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST1_cycif-tonsil-cycle2.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST1_cycif-tonsil-cycle2.ome-ffp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST2_cycif-tonsil-cycle3.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST2_cycif-tonsil-cycle3.ome-ffp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST2_cycif-tonsil-cycle1.ome-dfp.tiff"),
+                            ImageUtils.getImageMetadata("$outputDir/illumination_correction/basicpy/TEST2_cycif-tonsil-cycle1.ome-ffp.tiff")
                         ).match()
                     },
                     { assert workflow.success }

diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
@@ -504,6 +504,30 @@
                 "physicalSizeY": 1.0,
                 "physicalSizeZ": null
             },
+            {
+                "format": "Tagged Image File Format",
+                "type": "float",
+                "sizeX": 220,
+                "sizeY": 180,
+                "sizeZ": 1,
+                "sizeC": 4,
+                "sizeT": 1,
+                "physicalSizeX": 1.0,
+                "physicalSizeY": 1.0,
+                "physicalSizeZ": null
+            },
+            {
+                "format": "Tagged Image File Format",
+                "type": "float",
+                "sizeX": 220,
+                "sizeY": 180,
+                "sizeZ": 1,
+                "sizeC": 4,
+                "sizeT": 1,
+                "physicalSizeX": 1.0,
+                "physicalSizeY": 1.0,
+                "physicalSizeZ": null
+            },
             {
                 "format": "Tagged Image File Format",
                 "type": "float",
@@ -718,6 +742,30 @@
                 "physicalSizeY": 1.0,
                 "physicalSizeZ": null
             },
+            {
+                "format": "Tagged Image File Format",
+                "type": "float",
+                "sizeX": 220,
+                "sizeY": 180,
+                "sizeZ": 1,
+                "sizeC": 4,
+                "sizeT": 1,
+                "physicalSizeX": 1.0,
+                "physicalSizeY": 1.0,
+                "physicalSizeZ": null
+            },
+            {
+                "format": "Tagged Image File Format",
+                "type": "float",
+                "sizeX": 220,
+                "sizeY": 180,
+                "sizeZ": 1,
+                "sizeC": 4,
+                "sizeT": 1,
+                "physicalSizeX": 1.0,
+                "physicalSizeY": 1.0,
+                "physicalSizeZ": null
+            },
             {
                 "format": "Tagged Image File Format",
                 "type": "float",

diff --git a/workflows/mcmicro.nf b/workflows/mcmicro.nf
@@ -53,12 +53,12 @@ workflow MCMICRO {
 
             ch_samplesheet
                 .transpose()
-                .map { [[it[1].split('/')[-1][0..-5],it[0]], it[1]] }
+                .map { [[it[1].toString().split('/')[-1][0..-5],it[0]], it[1]] }
                 .set { ashlar_input_keyed }
 
-                ch_samplesheet
-                    .transpose()
-                    .set { ch_basicpy_input }
+            ch_samplesheet
+                .transpose()
+                .set { ch_basicpy_input }
 
             BASICPY(ch_basicpy_input)
             ch_versions = ch_versions.mix(BASICPY.out.versions)