Merge pull request #208 from luisas/fix_again_pr

Fix singularity config

Author: luisas

nextflow.config

@@ -123,22 +123,21 @@ profiles {
     }
     docker {
         docker.enabled          = true
-        docker.runOptions      = params.use_gpu ? '--gpus all' : '-u $(id -u):$(id -g)'
+        docker.runOptions       = params.use_gpu ? '--gpus all' : '-u $(id -u):$(id -g)'
         conda.enabled           = false
         singularity.enabled     = false
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
         apptainer.enabled       = false
-        docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm {
-        docker.runOptions     = params.use_gpu ? '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all' : '-u $(id -u):$(id -g) --platform=linux/amd64'
+        docker.runOptions       = params.use_gpu ? '-u $(id -u):$(id -g) --platform=linux/amd64 --gpus all' : '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
         singularity.enabled     = true
         singularity.autoMounts  = true
-        singularity.runOptions = params.use_gpu ? '--nv' : singularity.runOptions
+        singularity.runOptions  = params.use_gpu ? '--nv' : ""
         conda.enabled           = false
         docker.enabled          = false
         podman.enabled          = false
@@ -177,7 +176,7 @@ profiles {
     apptainer {
         apptainer.enabled       = true
         apptainer.autoMounts    = true
-        apptainer.runOptions    = params.use_gpu ? '--nv' : apptainer.runOptions
+        apptainer.runOptions    = params.use_gpu ? '--nv' : ""
         conda.enabled           = false
         docker.enabled          = false
         singularity.enabled     = false
@@ -236,7 +235,6 @@ charliecloud.registry = 'quay.io'
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
 // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
-
 env {
     PYTHONNOUSERSITE = 1
     R_PROFILE_USER   = "/.Rprofile"