From 28d895d78d17f8506ce976b09274451e2f655e32 Mon Sep 17 00:00:00 2001
From: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Date: Thu, 23 Apr 2026 12:45:07 +0000
Subject: [PATCH] Fix redundant containers

---
 modules/nf-core/clair3/main.nf                  | 4 +---
 modules/nf-core/traitar/pfamget/environment.yml | 1 -
 modules/nf-core/traitar/pfamget/main.nf         | 2 +-
 modules/nf-core/traitar/run/main.nf             | 2 +-
 4 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/clair3/main.nf b/modules/nf-core/clair3/main.nf
index a7d91f5c8aaf..48c90a44f7ff 100644
--- a/modules/nf-core/clair3/main.nf
+++ b/modules/nf-core/clair3/main.nf
@@ -3,9 +3,7 @@ process CLAIR3 {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-    'docker.io/hkubal/clair3:v2.0.0' :
-    'docker.io/hkubal/clair3:v2.0.0' }"
+    container "docker.io/hkubal/clair3:v2.0.0"
 
     input:
     tuple val(meta), path(bam), path(bai), val(packaged_model), path(user_model), val(platform)
diff --git a/modules/nf-core/traitar/pfamget/environment.yml b/modules/nf-core/traitar/pfamget/environment.yml
index 2dcfe899936a..0b657682e431 100644
--- a/modules/nf-core/traitar/pfamget/environment.yml
+++ b/modules/nf-core/traitar/pfamget/environment.yml
@@ -1,6 +1,5 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
diff --git a/modules/nf-core/traitar/pfamget/main.nf b/modules/nf-core/traitar/pfamget/main.nf
index babd16a3734b..e9b5013b86b8 100644
--- a/modules/nf-core/traitar/pfamget/main.nf
+++ b/modules/nf-core/traitar/pfamget/main.nf
@@ -4,7 +4,7 @@ process TRAITAR_PFAMGET {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:ccae2eabc2a54ac8' :
+        'oras://community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:9b929a08d061b63d' :
         'community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:ccae2eabc2a54ac8' }"
 
     output:
diff --git a/modules/nf-core/traitar/run/main.nf b/modules/nf-core/traitar/run/main.nf
index 7a1825399fa7..9e5fc95ff799 100644
--- a/modules/nf-core/traitar/run/main.nf
+++ b/modules/nf-core/traitar/run/main.nf
@@ -4,7 +4,7 @@ process TRAITAR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:ccae2eabc2a54ac8' :
+        'oras://community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:9b929a08d061b63d' :
         'community.wave.seqera.io/library/hmmer_prodigal_pandas_parallel_pruned:ccae2eabc2a54ac8' }"
 
     input: