Update module: propr/propd (#9296)

* Update module: propr/propd

* Update snapshots for abundance_differential_filter propd tests

Author: ninaxiong11

modules/nf-core/propr/propd/environment.yml

@@ -5,5 +5,5 @@ channels:
   - bioconda
 
 dependencies:
-  - bioconda::bioconductor-limma=3.58.1
-  - conda-forge::r-propr=5.1.6
+  - bioconda::bioconductor-limma=3.62.1
+  - conda-forge::r-propr=5.1.8

modules/nf-core/propr/propd/main.nf

@@ -4,8 +4,8 @@ process PROPR_PROPD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/27/276e08c149faa028a34ec65f74ac9eac58c2036a30db1f72acc9e35967936620/data' :
-        'community.wave.seqera.io/library/bioconductor-limma_r-propr:8d299a2da993327c' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/10/10bcda8d87b62771528894e1c03e0f38780e48f37e1bda146e81001a0d0054aa/data' :
+        'community.wave.seqera.io/library/bioconductor-limma_r-propr:4b3195a14835ef20' }"
 
     input:
     tuple val(meta), val(contrast_variable), val(reference), val(target)

modules/nf-core/propr/propd/tests/main.nf.test.snap

@@ -14,15 +14,15 @@
                 ]
             ],
             [
-                "versions.yml:md5,f356eb5d430713b086255dfc32b5d6ee"
+                "versions.yml:md5,a6e655144d7d1d743781538442685666"
             ],
             "treatment_mCherry_hND6_.propd.genewise.png"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-06-17T10:50:46.149119"
+        "timestamp": "2025-10-29T13:18:33.094065"
     },
     "Test propr/propd when using Box-cox transformation": {
         "content": [
@@ -39,15 +39,15 @@
                 ]
             ],
             [
-                "versions.yml:md5,f356eb5d430713b086255dfc32b5d6ee"
+                "versions.yml:md5,a6e655144d7d1d743781538442685666"
             ],
             "treatment_mCherry_hND6_.propd.genewise.png"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-06-17T10:51:46.832489"
+        "timestamp": "2025-10-29T13:19:24.03108"
     },
     "Test propr/propd when using permutation tests": {
         "content": [
@@ -72,19 +72,19 @@
                         "target": "hND6",
                         "blocking": ""
                     },
-                    "treatment_mCherry_hND6_.propd.fdr.tsv:md5,9c7011afa34a2ce7e33da9a6a6820c7e"
+                    "treatment_mCherry_hND6_.propd.fdr.tsv:md5,dca61ef4ab98984c2dcd884ce85feef8"
                 ]
             ],
             [
-                "versions.yml:md5,f356eb5d430713b086255dfc32b5d6ee"
+                "versions.yml:md5,a6e655144d7d1d743781538442685666"
             ],
             "treatment_mCherry_hND6_.propd.genewise.png"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-06-17T10:52:55.401249"
+        "timestamp": "2025-10-29T13:20:49.704914"
     },
     "Test propr/propd when saving all outputs": {
         "content": [
@@ -126,15 +126,15 @@
             ],
             null,
             [
-                "versions.yml:md5,f356eb5d430713b086255dfc32b5d6ee"
+                "versions.yml:md5,a6e655144d7d1d743781538442685666"
             ],
             "treatment_mCherry_hND6_.propd.genewise.png",
             "treatment_mCherry_hND6_.propd.rds"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-06-17T10:51:14.997099"
+        "timestamp": "2025-10-29T13:21:30.746294"
     }
 }

subworkflows/nf-core/abundance_differential_filter/tests/main.nf.test.snap

@@ -626,16 +626,16 @@
                 "versions.yml:md5,1a6a400c49aa4dda7ec5c4ed0cc56340",
                 "versions.yml:md5,1c02d4e455e8f3809c8ce37bee947690",
                 "versions.yml:md5,1ddaab440e2528c688c05a02dd066f12",
-                "versions.yml:md5,2a8f88e4b08dd4617efec4053ffa97f6",
                 "versions.yml:md5,2c0576aefff8da32c7c0cfd8529aa4b5",
-                "versions.yml:md5,b80e2c320ea0429466a7b7c3c3ac78fa"
+                "versions.yml:md5,b80e2c320ea0429466a7b7c3c3ac78fa",
+                "versions.yml:md5,ff5b7c1d83470f6f548f3643bb37a830"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-06-17T10:39:12.177003"
+        "timestamp": "2025-10-29T15:08:57.424485"
     },
     "stub": {
         "content": [
@@ -1185,13 +1185,13 @@
             ],
             [
                 "versions.yml:md5,1c02d4e455e8f3809c8ce37bee947690",
-                "versions.yml:md5,2a8f88e4b08dd4617efec4053ffa97f6"
+                "versions.yml:md5,ff5b7c1d83470f6f548f3643bb37a830"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.6"
         },
-        "timestamp": "2025-06-17T10:32:04.952546"
+        "timestamp": "2025-10-29T15:07:36.308435"
     }
 }