switch to container option

nf-core · Mar 11, 2024 · 142fb98 · 142fb98
1 parent 3811751
commit 142fb98
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/modules/local/ms2rescore.nf b/modules/local/ms2rescore.nf
@@ -8,7 +8,7 @@ process MS2RESCORE {
         'biocontainers/ms2rescore:3.0.1--pyhdfd78af_2' }"
 
     // userEmulation settings when docker is specified
-    //containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''
+    containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''
 
     input:
     tuple val(meta), path(idxml), path(mzml), path(fasta)

diff --git a/nextflow.config b/nextflow.config
@@ -167,10 +167,10 @@ profiles {
         shifter.enabled          = false
         charliecloud.enabled     = false
         apptainer.enabled        = false
-        docker.runOptions        = '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME'
+        process.containerOptions = '-u $(id -u):$(id -g)'
     }
     arm {
-        docker.runOptions        = '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME --platform=linux/amd64'
+        process.containerOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
         singularity.enabled    = true