Merge pull request #1019 from maxulysse/patch-registry

Set a default registry outside of profile scope

CHANGELOG.md

@@ -38,6 +38,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#968](https://github.com/nf-core/sarek/pull/968) - Update all modules
 - [#1014](https://github.com/nf-core/sarek/pull/1014) - `snpeff_db` is now only the `db` version and not `genome.db`
 - [#1015](https://github.com/nf-core/sarek/pull/1015) - Increase default value for `--nucleotides_per_second` to `200000` resulting in 21 groups for `GATK.GRCh38`
+- [#1019](https://github.com/nf-core/sarek/pull/1019) - Set a default registry outside of profile scope
 
 ### Fixed
 

nextflow.config

@@ -175,7 +175,6 @@ profiles {
         charliecloud.enabled   = false
         conda.enabled          = false
         docker.enabled         = true
-        docker.registry        = 'quay.io'
         docker.userEmulation   = { params.use_gatk_spark ? false : true }.call()
         podman.enabled         = false
         shifter.enabled        = false
@@ -200,7 +199,6 @@ profiles {
         conda.enabled          = false
         docker.enabled         = false
         podman.enabled         = true
-        podman.registry        = 'quay.io'
         shifter.enabled        = false
         singularity.enabled    = false
     }
@@ -289,6 +287,12 @@ env {
 // Capture exit codes from upstream processes when piping
 process.shell = ['/bin/bash', '-euo', 'pipefail']
 
+// Set default registry for Docker and Podman independent of -profile
+// Will not be used unless Docker / Podman are enabled
+// Set to your registry if you have a mirror of containers
+docker.registry = 'quay.io'
+podman.registry = 'quay.io'
+
 def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
 timeline {
     enabled = true