Updating container directives.

modules/local/arborator/main.nf

@@ -9,7 +9,7 @@ process ARBORATOR {
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/arborator%3A1.0.0--pyhdfd78af_1' :
-    'quay.io/biocontainers/arborator:1.0.0--pyhdfd78af_1' }"
+    'biocontainers/arborator:1.0.0--pyhdfd78af_1' }"
 
     input:
     path merged_profiles // The allelic profiles

modules/local/arborview.nf

@@ -9,8 +9,10 @@ process ARBOR_VIEW {
     stageInMode 'copy' // Need to copy in arbor view html
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-    "docker.io/python:3.11.6" :
-    "docker.io/python:3.11.6" }"
+    'docker.io/python:3.11.6' :
+    task.ext.override_configured_container_registry != false ? 
+    'docker.io/python:3.11.6' : 
+    'python:3.11.6' }"
 
     input:
     tuple val(cluster_group), path(tree), path(contextual_data)

modules/local/locidex/merge/main.nf

@@ -8,7 +8,7 @@ process LOCIDEX_MERGE {
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
     'https://depot.galaxyproject.org/singularity/locidex:0.1.1--pyhdfd78af_0' :
-    'quay.io/biocontainers/locidex:0.1.1--pyhdfd78af_0' }"
+    'biocontainers/locidex:0.1.1--pyhdfd78af_0' }"
 
     input:
     path input_values // [file(sample1), file(sample2), file(sample3), etc...]

nextflow.config

@@ -165,6 +165,9 @@ docker.registry      = 'quay.io'
 podman.registry      = 'quay.io'
 singularity.registry = 'quay.io'
 
+// Override the default Docker registry when required
+process.ext.override_configured_container_registry = true
+
 // Nextflow plugins
 plugins {
     id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet