Removing docker.userEmulation

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

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

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.

nextflow.config

@@ -190,10 +190,9 @@ 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)'
+        docker.runOptions      = '--platform=linux/amd64 -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME -u $(id -u):$(id -g)'
         singularity.enabled    = false
     }
     arm {

tests/test_gatk4spark.yml

@@ -3,6 +3,7 @@
   tags:
     - gatk4spark
     - preprocessing
+    - foo
   files:
     - path: results/csv/markduplicates.csv
       md5sum: 0dec46c4dc83acc263efc234805e9349

tests/test_joint_germline.yml

@@ -4,6 +4,7 @@
     - germline
     - joint_germline
     - variant_calling
+    - foo
   files:
     - path: results/csv/variantcalled.csv
       md5sum: d2dffdbd2b4f1f26a06637592d24dab3