Merge pull request nf-core#1405 from asp8200/remove_docker_userEmulation

Removing docker.userEmulation
asp8200 · Feb 23, 2024 · 12d0867 · 12d0867
2 parents 3893bb5 + ac80ab9
commit 12d0867
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Showing 5 changed files with 2 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -42,6 +42,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Removed
 
+- [#1405](https://github.com/nf-core/sarek/pull/1405) - Removing docker.userEmulation
+
 ### Dependencies
 
 | Dependency | Old version | New version |

diff --git a/conf/test.config b/conf/test.config
@@ -108,7 +108,6 @@ if (System.getenv('PROFILE')) {
     } else if ("$PROFILE" == "docker") {
         conda.enabled                            = false
         docker.enabled                           = true
-        docker.userEmulation                     = { params.use_gatk_spark ? false : true }.call()
         charliecloud.enabled                     = false
         podman.enabled                           = false
         shifter.enabled                          = false

diff --git a/conf/test/cache.config b/conf/test/cache.config
@@ -116,7 +116,6 @@ if (System.getenv('PROFILE')) {
     } else if ("$PROFILE" == "docker") {
         conda.enabled                            = false
         docker.enabled                           = true
-        docker.userEmulation                     = { params.use_gatk_spark ? false : true }.call()
         charliecloud.enabled                     = false
         podman.enabled                           = false
         shifter.enabled                          = false

diff --git a/docs/usage.md b/docs/usage.md
@@ -769,10 +769,6 @@ Re-start your session.
 
 Note that the way to increase the open file limit in your system may be slightly different or require additional steps.
 
-### Cannot delete work folder when using docker + Spark
-
-Currently, when running spark-based tools in combination with docker, it is required to set `docker.userEmulation = false`. This can unfortunately causes permission issues when `work/` is being written with root permissions. In case this happens, you might need to configure docker to run without `userEmulation` (see [here](https://github.com/Midnighter/nf-core-adr/blob/main/docs/adr/0008-refrain-from-using-docker-useremulation-in-nextflow.md)).
-
 ## How to handle UMIs
 
 Sarek can process UMI-reads, using [fgbio](http://fulcrumgenomics.github.io/fgbio/tools/latest/) tools.

diff --git a/nextflow.config b/nextflow.config
@@ -190,7 +190,6 @@ profiles {
         charliecloud.enabled   = false
         conda.enabled          = false
         docker.enabled         = true
-        docker.userEmulation   = { params.use_gatk_spark ? false : true }.call()
         podman.enabled         = false
         shifter.enabled        = false
         docker.runOptions      = '-u $(id -u):$(id -g)'