diff --git a/CHANGELOG.md b/CHANGELOG.md index 6f786c1d9c..01033c6d4a 100644 --- 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 index 0852c5b542..28bd2f7bf3 100644 --- a/conf/test.config +++ b/conf/test.config @@ -108,7 +108,6 @@ if (System.getenv('PROFILE')) { } else if ("$PROFILE" == "docker") { conda.enabled = false docker.enabled = true - docker.userEmulation = { params.use_gatk_spark ? false : true }.call() charliecloud.enabled = false podman.enabled = false shifter.enabled = false diff --git a/conf/test/cache.config b/conf/test/cache.config index 12853ad129..f6d0ceca79 100644 --- a/conf/test/cache.config +++ b/conf/test/cache.config @@ -116,7 +116,6 @@ if (System.getenv('PROFILE')) { } else if ("$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 index b6c2aba974..fbd3e8d9a6 100644 --- 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 index d49a3ceeff..c0eb9c702c 100644 --- 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)'