fixed meta and xenium bundle file path

nf-core · Oct 30, 2024 · 549908c · 549908c
1 parent e5a10b1
commit 549908c
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Showing 15 changed files with 81 additions and 75 deletions.
diff --git a/modules/nf-core/xeniumranger/import-segmentation/main.nf b/modules/nf-core/xeniumranger/import-segmentation/main.nf
@@ -5,8 +5,7 @@ process XENIUMRANGER_IMPORT_SEGMENTATION {
     container "nf-core/xeniumranger:3.0.1"
 
     input:
-    val(meta)
-    path(xenium_bundle)
+    tuple val(meta), path(xenium_bundle)
     val(expansion_distance)
     path(coordinate_transform)
     path(nuclei)

diff --git a/modules/nf-core/xeniumranger/import-segmentation/meta.yml b/modules/nf-core/xeniumranger/import-segmentation/meta.yml
@@ -29,7 +29,7 @@ input:
         description: |
           Groovy Map containing run information
           e.g. [id:'xenium_bundle_path']
-  - - xenium_bundle:
+    - xenium_bundle:
         type: directory
         description: Path to the xenium output bundle generated by the Xenium Onboard
           Analysis pipeline

diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test
@@ -26,14 +26,15 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_import-segmentation"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
-                input[2] = 0
-                input[3] = []
-                input[4] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/nuclei.npy"
+                input[0] = Channel.of([
+                        [id: "test_xeniumranger_relabel"],
+                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = 0
+                input[2] = []
+                input[3] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/nuclei.npy"
+                input[4] = []
                 input[5] = []
                 input[6] = []
-                input[7] = []
                 """
             }
         }
@@ -92,14 +93,15 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_import-segmentation"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
-                input[2] = 0
-                input[3] = []
-                input[4] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/nuclei.npy"
+                input[0] = Channel.of([
+                        [id: "test_xeniumranger_relabel"],
+                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = 0
+                input[2] = []
+                input[3] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/nuclei.npy"
+                input[4] = []
                 input[5] = []
                 input[6] = []
-                input[7] = []
                 """
             }
         }
@@ -157,14 +159,15 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_import-segmentation"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
-                input[2] = 0
-                input[3] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/imagealignment.csv"
+                input[0] = Channel.of([
+                        [id: "test_xeniumranger_relabel"],
+                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = 0
+                input[2] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/imagealignment.csv"
+                input[3] = []
                 input[4] = []
-                input[5] = []
-                input[6] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/segmentation.csv"
-                input[7] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/segmentation_polygons.json"
+                input[5] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/segmentation.csv"
+                input[6] = UNZIP.out.unzipped_archive.map { it[1] } + "/segmentations/segmentation_polygons.json"
                 """
             }
         }
@@ -222,14 +225,15 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_import-segmentation"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
-                input[2] = 0
-                input[3] = []
-                input[4] = UNZIP.out.unzipped_archive.map { it[1] } + "/cells.zarr.zip"
+                input[0] = Channel.of([
+                        [id: "test_xeniumranger_relabel"],
+                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = 0
+                input[2] = []
+                input[3] = UNZIP.out.unzipped_archive.map { it[1] } + "/cells.zarr.zip"
+                input[4] = []
                 input[5] = []
                 input[6] = []
-                input[7] = []
                 """
             }
         }
@@ -288,14 +292,15 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_import-segmentation"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
-                input[2] = 0
-                input[3] = []
-                input[4] = UNZIP.out.unzipped_archive.map { it[1] } + "/cells.zarr.zip"
+                input[0] = Channel.of([
+                        [id: "test_xeniumranger_relabel"],
+                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = 0
+                input[2] = []
+                input[3] = UNZIP.out.unzipped_archive.map { it[1] } + "/cells.zarr.zip"
+                input[4] = []
                 input[5] = []
                 input[6] = []
-                input[7] = []
                 """
             }
         }

diff --git a/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap
@@ -74,7 +74,7 @@
                 "0": [
                     [
                         {
-                            "id": "test_xeniumranger_import-segmentation"
+                            "id": "test_xeniumranger_relabel"
                         },
                         "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -85,7 +85,7 @@
                 "outs": [
                     [
                         {
-                            "id": "test_xeniumranger_import-segmentation"
+                            "id": "test_xeniumranger_relabel"
                         },
                         "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -99,7 +99,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-22T20:05:05.394111"
+        "timestamp": "2024-10-30T12:55:58.357065"
     },
     "xeniumranger import-segmentation nuclei tif": {
         "content": [

diff --git a/modules/nf-core/xeniumranger/relabel/main.nf b/modules/nf-core/xeniumranger/relabel/main.nf
@@ -5,8 +5,7 @@ process XENIUMRANGER_RELABEL {
     container "nf-core/xeniumranger:3.0.1"
 
     input:
-    val(meta)
-    path(xenium_bundle)
+    tuple val(meta), path(xenium_bundle)
     path(gene_panel)
 
     output:

diff --git a/modules/nf-core/xeniumranger/relabel/meta.yml b/modules/nf-core/xeniumranger/relabel/meta.yml
@@ -23,7 +23,7 @@ input:
         description: |
           Groovy Map containing run information
           e.g. [id:'xenium_bundle_path']
-  - - xenium_bundle:
+    - xenium_bundle:
         type: directory
         description: Path to the xenium output bundle generated by the Xenium Onboard
           Analysis pipeline

diff --git a/modules/nf-core/xeniumranger/relabel/tests/main.nf.test b/modules/nf-core/xeniumranger/relabel/tests/main.nf.test
@@ -26,9 +26,10 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_relabel"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
-                input[2] = UNZIP.out.unzipped_archive.map { it[1] } + "/gene_panel.json"
+                input[0] = Channel.of([
+                        [id: "test_xeniumranger_relabel"],
+                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = UNZIP.out.unzipped_archive.map { it[1] } + "/gene_panel.json"
                 """
             }
         }
@@ -66,7 +67,6 @@ nextflow_process {
                 { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'variance.csv' }).exists() },
                 { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'metrics_summary.csv' }).exists() },
                 { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'clusters.csv' }).exists() },
-
             )
         }
     }
@@ -76,9 +76,10 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_relabel"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
-                input[2] = UNZIP.out.unzipped_archive.map { it[1] } + "/gene_panel.json"
+                input[0] = Channel.of([
+                        [id: "test_xeniumranger_relabel"],
+                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = UNZIP.out.unzipped_archive.map { it[1] } + "/gene_panel.json"
                 """
             }
         }

diff --git a/modules/nf-core/xeniumranger/rename/main.nf b/modules/nf-core/xeniumranger/rename/main.nf
@@ -5,8 +5,7 @@ process XENIUMRANGER_RENAME {
     container "nf-core/xeniumranger:3.0.1"
 
     input:
-    val(meta)
-    path(xenium_bundle)
+    tuple val(meta), path(xenium_bundle)
     val(region_name)
     val(cassette_name)
 

diff --git a/modules/nf-core/xeniumranger/rename/meta.yml b/modules/nf-core/xeniumranger/rename/meta.yml
@@ -22,7 +22,7 @@ input:
   - - meta:
         type: map
         description: Groovy Map containing sample information e.g. [ id:'test' ]
-  - - xenium_bundle:
+    - xenium_bundle:
         type: directory
         description: Path to the xenium output bundle generated by the Xenium Onboard
           Analysis pipeline

diff --git a/modules/nf-core/xeniumranger/rename/tests/main.nf.test b/modules/nf-core/xeniumranger/rename/tests/main.nf.test
@@ -26,10 +26,11 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_rename"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
-                input[2] = "test_region"
-                input[3] = "test_cassette"
+                input[0] = Channel.of([
+                            [id: "test_xeniumranger_relabel"],
+                        ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = "test_region"
+                input[2] = "test_cassette"
                 """
             }
         }
@@ -58,10 +59,11 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_rename"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
-                input[2] = "test_region"
-                input[3] = "test_cassette"
+                input[0] = Channel.of([
+                            [id: "test_xeniumranger_relabel"],
+                        ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = "test_region"
+                input[2] = "test_cassette"
                 """
             }
         }

diff --git a/modules/nf-core/xeniumranger/rename/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/rename/tests/main.nf.test.snap
@@ -5,7 +5,7 @@
                 "0": [
                     [
                         {
-                            "id": "test_xeniumranger_rename"
+                            "id": "test_xeniumranger_relabel"
                         },
                         "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -16,7 +16,7 @@
                 "outs": [
                     [
                         {
-                            "id": "test_xeniumranger_rename"
+                            "id": "test_xeniumranger_relabel"
                         },
                         "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -30,7 +30,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-22T20:12:43.026607"
+        "timestamp": "2024-10-30T12:00:02.547585"
     },
     "xeniumranger rename": {
         "content": [
@@ -47,7 +47,7 @@
                 "cells.parquet:md5,e1450c7eca3d7ce0d4911c95042b1303",
                 "cells.zarr.zip:md5,556e47d5b14150239b10b2f801defa2b",
                 "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde",
-                "metrics_summary.csv:md5,54ad3944eb3ba6a4d7bda01bc2a6bb1c",
+                "metrics_summary.csv:md5,ce5c0c32c2a6994dd29e1595b439125b",
                 "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b",
                 "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98",
                 "nucleus_boundaries.csv.gz:md5,e417b6e293298870956d42c7106cbd0c",
@@ -60,6 +60,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-23T18:41:44.42271"
+        "timestamp": "2024-10-30T11:59:45.587263"
     }
 }
diff --git a/modules/nf-core/xeniumranger/resegment/main.nf b/modules/nf-core/xeniumranger/resegment/main.nf
@@ -5,8 +5,7 @@ process XENIUMRANGER_RESEGMENT {
     container "nf-core/xeniumranger:3.0.1"
 
     input:
-    val(meta)
-    path(xenium_bundle)
+    tuple val(meta), path(xenium_bundle)
     val(expansion_distance)
     val(dapi_filter)
     val(boundary_stain)

diff --git a/modules/nf-core/xeniumranger/resegment/meta.yml b/modules/nf-core/xeniumranger/resegment/meta.yml
@@ -22,7 +22,7 @@ input:
         description: |
           Groovy Map containing run information
           e.g. [ id:'xenium_experiment' ]
-  - - xenium_bundle:
+    - xenium_bundle:
         type: directory
         description: Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline
   - - expansion_distance:

diff --git a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test
@@ -26,12 +26,13 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_resegment"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
+                input[0] = Channel.of([
+                        [id: "test_xeniumranger_relabel"],
+                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = []
                 input[2] = []
                 input[3] = []
                 input[4] = []
-                input[5] = []
                 """
             }
         }
@@ -56,12 +57,13 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [id: "test_xeniumranger_resegment"]
-                input[1] = UNZIP.out.unzipped_archive.map { it[1] }
+                input[0] = Channel.of([
+                        [id: "test_xeniumranger_relabel"],
+                    ]).combine(UNZIP.out.unzipped_archive.map { it[1] })
+                input[1] = []
                 input[2] = []
                 input[3] = []
                 input[4] = []
-                input[5] = []
                 """
             }
         }

diff --git a/modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap b/modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap
@@ -5,7 +5,7 @@
                 "0": [
                     [
                         {
-                            "id": "test_xeniumranger_resegment"
+                            "id": "test_xeniumranger_relabel"
                         },
                         "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -16,7 +16,7 @@
                 "outs": [
                     [
                         {
-                            "id": "test_xeniumranger_resegment"
+                            "id": "test_xeniumranger_relabel"
                         },
                         "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
@@ -30,6 +30,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-28T14:02:23.13186"
+        "timestamp": "2024-10-30T12:23:55.768779"
     }
 }