Merge branch 'nf-core:master' into master

Author: jfy133

.github/actions/get-shards/action.yml

@@ -26,10 +26,10 @@ runs:
         java-version: "17"
 
     - name: Set up nf-test
-      uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: ${{ env.NFT_VER }}
-        install-pdiff: true
+        install-fast-diff: true
 
     - name: Get number of shards
       id: shards

.github/actions/nf-test-action/action.yml

@@ -37,10 +37,10 @@ runs:
         python-version: "3.14"
 
     - name: Set up nf-test
-      uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2
+      uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
       with:
         version: "${{ env.NFT_VER }}"
-        install-pdiff: true
+        install-fast-diff: true
 
     - name: Set up apptainer
       if: contains(inputs.profile, 'singularity')
@@ -56,7 +56,7 @@ runs:
 
     - name: Set up Conda
       if: ${{contains(inputs.profile, 'conda')}}
-      uses: conda-incubator/setup-miniconda@fc2d68f6413eb2d87b895e92f8584b5b94a10167 # v3
+      uses: conda-incubator/setup-miniconda@8ee1f361103df19b6f8c8655fd3967a8ecb162d5 # v4
       with:
         auto-update-conda: true
         conda-solver: libmamba

.github/workflows/update-gpu-snapshot.yml

@@ -71,10 +71,10 @@ jobs:
           python-version: "3.14"
 
       - name: Set up nf-test
-        uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2
+        uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
         with:
           version: "${{ env.NFT_VER }}"
-          install-pdiff: true
+          install-fast-diff: true
 
       - name: Update gpu snapshot
         id: update-gpu-snapshot

.github/workflows/update-sentieon-snapshot.yml

@@ -74,10 +74,10 @@ jobs:
           python-version: "3.14"
 
       - name: Set up nf-test
-        uses: nf-core/setup-nf-test@ce65500579e8587607aab289ecb3a9c343c32e79 # v2
+        uses: nf-core/setup-nf-test@4069fbbaabe94c08faba4ad261bfa88225ba133f # v2
         with:
           version: "${{ env.NFT_VER }}"
-          install-pdiff: true
+          install-fast-diff: true
 
       # Set up secrets
       - name: Set up Nextflow secrets

modules/nf-core/affy/justrma/main.nf

@@ -3,9 +3,9 @@ process AFFY_JUSTRMA {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bioconductor-affy:1.78.0--r43ha9d7317_1':
-        'quay.io/biocontainers/bioconductor-affy:1.78.0--r43ha9d7317_1' }"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/62/62d22bc460807a1a4ded40e5b7a391aa6f2dac189d4153d684472d65333ca8d4/data':
+        'community.wave.seqera.io/library/bioconductor-affy_r-base:dd8a5ecd6fc301b3' }"
 
     input:
     tuple val(meta), path(samplesheet), path(celfiles_dir)

modules/nf-core/ampcombi2/cluster/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::ampcombi=2.0.1
+  - bioconda::ampcombi=3.0.0

modules/nf-core/ampcombi2/cluster/main.nf

@@ -4,8 +4,8 @@ process AMPCOMBI2_CLUSTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
-        'quay.io/biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ampcombi:3.0.0--pyhdfd78af_0':
+        'quay.io/biocontainers/ampcombi:3.0.0--pyhdfd78af_0' }"
 
     input:
     path(summary_file)

modules/nf-core/ampcombi2/cluster/meta.yml

@@ -14,9 +14,9 @@ tools:
   - ampcombi2/cluster:
       description: "A tool for clustering all AMP hits found across many samples and
         supporting many AMP prediction tools."
-      homepage: "https://github.com/Darcy220606/AMPcombi"
-      documentation: "https://github.com/Darcy220606/AMPcombi"
-      tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev"
+      homepage: "https://github.com/paleobiotechnology/AMPcombi"
+      documentation: "https://ampcombi.readthedocs.io"
+      tool_dev_url: "https://github.com/paleobiotechnology/AMPcombi/tree/dev"
       licence: ["MIT"]
       identifier: ""
 
@@ -80,3 +80,4 @@ authors:
   - "@darcy220606"
 maintainers:
   - "@darcy220606"
+  - "@jasmezz"

modules/nf-core/ampcombi2/cluster/tests/main.nf.test.snap

@@ -8,14 +8,14 @@
                     [
                         "AMPCOMBI2_CLUSTER",
                         "ampcombi",
-                        "2.0.1"
+                        "3.0.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-11T15:43:28.198864",
+        "timestamp": "2026-04-23T19:25:25.611433665",
         "meta": {
-            "nf-test": "0.9.4",
+            "nf-test": "0.9.5",
             "nextflow": "25.10.4"
         }
     },
@@ -35,14 +35,14 @@
                     [
                         "AMPCOMBI2_CLUSTER",
                         "ampcombi",
-                        "2.0.1"
+                        "3.0.0"
                     ]
                 ]
             }
         ],
-        "timestamp": "2026-03-11T15:43:38.459512",
+        "timestamp": "2026-04-23T19:25:56.951391865",
         "meta": {
-            "nf-test": "0.9.4",
+            "nf-test": "0.9.5",
             "nextflow": "25.10.4"
         }
     }

modules/nf-core/ampcombi2/complete/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::ampcombi=2.0.1
+  - bioconda::ampcombi=3.0.0